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Opened 4 days ago
Last modified 4 days ago
#20135 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x000000031e473000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d467000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c45b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b44f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a443000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000319437000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031842b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031741f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000316413000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000315407000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003143fb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003133ef000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003123e3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f088a0c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, lxml._elementpath, lxml.etree, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast (total: 62)
{"app_name":"ChimeraX","timestamp":"2026-04-03 18:31:30.00 -0400","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6.1 (24G90)","roots_installed":0,"name":"ChimeraX","incident_id":"9F2F327E-7A28-45FF-A622-C2AE24F97A58"}
{
"uptime" : 2800000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1816534185,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 459761,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2026-04-03 18:27:59.3865 -0400",
"codeSigningMonitor" : 1,
"incident" : "9F2F327E-7A28-45FF-A622-C2AE24F97A58",
"pid" : 61659,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-03-17 15:49:30.4754 -0400",
"procStartAbsTime" : 60473543095781,
"procExitAbsTime" : 68091359552862,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0C2BB12E-24B4-5BE2-9EF3-072FD0ADFDC2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FA6EEC6E-A890-96AC-901B-4A3BA4995AFD",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "52F873D9-CF35-4D9E-BD7E-324140C9F0A7",
"wakeTime" : 5864,
"sleepWakeUUID" : "68DA9BE4-907D-474B-AD6B-8834A1041833",
"sip" : "enabled",
"vmRegionInfo" : "0x5d790b31a318 is not in any region. Bytes after previous region: 102293423891225 Bytes before following region: 2778656038120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00005d790b31a318","rawCodes":[1,102774460228376],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00005d790b31a318"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61659},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x5d790b31a318 is not in any region. Bytes after previous region: 102293423891225 Bytes before following region: 2778656038120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4697914008},{"value":99},{"value":116},{"value":1153027057775048320},{"value":1027},{"value":13469539983515972068},{"value":13469539991309472036},{"value":14757395258967641293},{"value":4294967286},{"value":4697913938},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8347587928},{"value":0},{"value":11},{"value":259},{"value":8330453408,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4357441072,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8291618816,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8291618816,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6485407884},"cpsr":{"value":1073745920},"fp":{"value":4697914080},"sp":{"value":4697914048},"esr":{"value":1442840704,"description":" Address 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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=4.8G written=103.6M(2%) resident=2972K(0%) swapped_out=100.7M(2%) unallocated=4.7G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 2544K 64 \nCG raster data 384K 8 \nColorSync 704K 38 \nCoreAnimation 3136K 152 \nCoreGraphics 656K 41 \nCoreServices 624K 2 \nCoreUI image data 3776K 33 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 3.8G 126 \nMALLOC guard page 288K 18 \nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 832K 52 \nStack 401.8M 53 \nStack Guard 56.0M 1 \nVM_ALLOCATE 414.4M 499 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 5521K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 34.4M 1096 \n__DATA_CONST 37.1M 1113 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 649.0M 163 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1128 \n__TEXT (graphics) 1200K 5 \n__TPRO_CONST 128K 2 \ndyld private memory 4128K 35 \nmapped file 311.0M 82 \npage table in kernel 2972K 1 \nshared memory 3152K 23 \n=========== ======= ======= \nTOTAL 7.3G 6743 \nTOTAL, minus reserved VM space 7.2G 6743 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "1df040d3026c31c32a32d1b43bdb250b448109b0",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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{
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_0.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_1.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_2.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_3.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_3.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_4.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_4.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_0.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_1.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_1.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_2.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_2.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_3.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_3.cif #9
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_4.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_4.cif #10
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_0.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_0.cif #11
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_1.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_1.cif #12
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_2.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_2.cif #13
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_3.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_3.cif #14
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_4.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_4.cif #15
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-15 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_1.cif, chain D (#2), sequence alignment score =
1469.5
RMSD between 112 pruned atom pairs is 0.263 angstroms; (across all 274 pairs:
20.703)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_2.cif, chain D (#3), sequence alignment score =
1469.5
RMSD between 158 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
18.950)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_3.cif, chain D (#4), sequence alignment score =
1460.5
RMSD between 152 pruned atom pairs is 0.237 angstroms; (across all 274 pairs:
20.473)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_4.cif, chain D (#5), sequence alignment score =
1451.5
RMSD between 141 pruned atom pairs is 0.178 angstroms; (across all 274 pairs:
19.690)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_0.cif, chain D (#6), sequence alignment score =
1288.3
RMSD between 177 pruned atom pairs is 0.529 angstroms; (across all 274 pairs:
12.666)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_1.cif, chain D (#7), sequence alignment score =
1297.3
RMSD between 176 pruned atom pairs is 0.520 angstroms; (across all 274 pairs:
10.517)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_2.cif, chain D (#8), sequence alignment score =
1295.5
RMSD between 178 pruned atom pairs is 0.578 angstroms; (across all 274 pairs:
10.087)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_3.cif, chain D (#9), sequence alignment score =
1300.9
RMSD between 177 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
10.467)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_4.cif, chain D (#10), sequence alignment score =
1284.7
RMSD between 176 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
13.215)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_0.cif, chain D (#11), sequence alignment score =
1449.7
RMSD between 179 pruned atom pairs is 0.451 angstroms; (across all 274 pairs:
7.791)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_1.cif, chain D (#12), sequence alignment score =
1453.3
RMSD between 179 pruned atom pairs is 0.374 angstroms; (across all 274 pairs:
10.016)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_2.cif, chain D (#13), sequence alignment score =
1464.1
RMSD between 181 pruned atom pairs is 0.296 angstroms; (across all 274 pairs:
8.969)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_3.cif, chain D (#14), sequence alignment score =
1471.3
RMSD between 172 pruned atom pairs is 0.272 angstroms; (across all 274 pairs:
15.272)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_4.cif, chain D (#15), sequence alignment score =
1458.7
RMSD between 165 pruned atom pairs is 0.463 angstroms; (across all 274 pairs:
19.186)
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> color #1 bychain
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #1 models
> delete atoms #2-5
> delete bonds #2-5
> show #1 models
> hide #1 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> ui tool show "Color Actions"
> set bgColor white
> hide #7 models
> hide #8 models
> show #8 models
> show #7 models
> show #6-10 surfaces
> select /C
740 atoms, 730 bonds, 99 residues, 11 models selected
> hide sel & #!6-10 surfaces
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide sel & #!6 surfaces
> select clear
> hide #!6 surfaces
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!6-10 surfaces
> select /D
24787 atoms, 25498 bonds, 3034 residues, 11 models selected
> show sel & #!6-10 surfaces
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!7 models
> hide #!6 models
> show #!8 models
> hide #!7 models
> show #!10 models
> hide #!8 models
> show #11 models
> hide #!10 models
> hide #11 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide sel & #!6-10 surfaces
> hide #!6 models
> delete atoms (#!7-10 & sel)
> delete bonds (#!7-10 & sel)
> undo
> select clear
> hide #!6 models
> undo
> hide #!6 models
> delete atoms #7-10
> delete bonds #7-10
> show #!6 models
> show #11 models
> hide #!6 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> show #11 models
> hide #15 models
> show #15 models
> hide #11 models
> show #11 models
> show #12 models
> hide #15 models
> show #13 models
> hide #12 models
> show #12 models
> hide #11 models
> show #14 models
> hide #12 models
> hide #13 models
> hide #14 models
> show #!6 models
> show #11 models
> show #12 models
> hide #!6 models
> hide #11 models
> hide #12 models
> show #11 models
> color #11 bychain
> show #15 models
> hide #11 models
> color #15 bychain
> show #!6 models
> hide #15 models
> color #!6 bychain
> show #1 models
> hide #1 models
> show #11 models
> hide #!6 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> show #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #6/B
Alignment identifier is 6/B
> select
> #6/A:4-7,10-14,19-25,32-37,43-48,52-56,59-64,69-74,83-90,97-99,103-108
501 atoms, 502 bonds, 62 residues, 1 model selected
> select #6/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:87-99
99 atoms, 100 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> set bgColor indian red
> set bgColor white
> color sel brown target acsp
> color sel crimson target acsp
> color sel dark red target acsp
> select #6/B:5-7,10-14,19-24,31-37,44-50,53-56,65-67,73-78,87-94,106-111
465 atoms, 466 bonds, 55 residues, 1 model selected
> select #6/B:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:91-102
92 atoms, 93 bonds, 12 residues, 1 model selected
> select #6/B:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:91-102
92 atoms, 93 bonds, 12 residues, 1 model selected
> color sel maroon target acsp
> select #6/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:87-99
99 atoms, 100 bonds, 13 residues, 1 model selected
> color sel medium slate blue target acsp
> color sel indigo target acsp
> color sel medium blue target acsp
> select clear
> select /A:87-:99
Expected an objects specifier or a keyword
> select /A:87-99
693 atoms, 700 bonds, 91 residues, 7 models selected
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #1 models
> color sel medium blue target acsp
> select /B:91-102
644 atoms, 651 bonds, 84 residues, 7 models selected
> color sel maroon target acsp
> hide #!6 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> show #!6 models
> hide #1 models
> show #11 models
> hide #!6 models
> show #12 models
> hide #11 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #!6 models
> hide #15 models
> show #15 models
> hide #15 models
> hide #!6 models
> show #12 models
> show #13 models
> show #14 models
> delete atoms (#12-14 & sel)
> delete bonds (#12-14 & sel)
> select clear
> undo
> show #11 models
> hide #!12 models
> hide #!13 models
> show #15 models
> hide #!14 models
> hide #15 models
> select clear
> show #!12 models
> hide #11 models
> show #!13 models
> show #!14 models
> delete atoms #12-14
> delete bonds #12-14
> show #!6 models
> show #11 models
> hide #!6 models
> show #!6 models
> hide #11 models
> show #11 models
> hide #!6 models
> show #15 models
> hide #11 models
> show #11 models
> hide #15 models
> show #15 models
> hide #11 models
> show #!6 models
> hide #15 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/TCR-
> peptide.cxs
opened ChimeraX session
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.contacts.cxs
opened ChimeraX session
> hide #3 models
> hide #6 models
> show #6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #3 models
> select #6/A:5,15
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95
109 atoms, 98 bonds, 13 residues, 1 model selected
> color sel magenta target acsp
> color sel violet target acsp
> color sel magenta target acsp
> color sel light steel blue target acsp
> color sel sky blue target acsp
> color sel cyan target acsp
> color sel magenta target acsp
> select clear
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> ui tool show "Color Actions"
> color sel magenta target acsp
> select clear
> show #3,6 surfaces
> hide #!3 models
> show #!3 models
> hide #!3,6 surfaces
> show #!1 models
> hide #!1 models
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> show sel atoms
> select clear
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select #6/A:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select clear
> transparency #3,6 70
> transparency #3,6 40
Drag select of 1 residues
> hide sel surfaces
> select clear
> hide #!3,6 surfaces
> show #!3,6 surfaces
> hide #!3,6 surfaces
> select #6/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel surfaces
> color (#!6 & sel) blue
> show sel surfaces
> select clear
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.png"
> width 900 height 668 supersample 4 transparentBackground true
> select #6/G:49@OG1
1 atom, 1 residue, 1 model selected
Drag select of fold_hqba_hfqx6_co_model_0.cif_B SES surface, 234 of 122862
triangles
> select #6/A:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #6/A:98
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #6/A:102
24 atoms, 21 bonds, 3 residues, 2 models selected
> select add #6/A:103
35 atoms, 32 bonds, 4 residues, 2 models selected
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> show sel surfaces
> hide #!3 models
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!6 surfaces
> show #!3 models
> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167
133 atoms, 122 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale violet red target acsp
> select clear
> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167
133 atoms, 122 bonds, 15 residues, 1 model selected
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select clear
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #6/A:41
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!6 & sel) magenta
> select up
38 atoms, 38 bonds, 5 residues, 2 models selected
> select up
1311 atoms, 1341 bonds, 167 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!3,6 surfaces
> undo
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.2.png"
> width 900 height 668 supersample 4 transparentBackground true
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif
Chain information for fold_hqba_yhbp_co_model_0.cif #4
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
Chain information for fold_hqba_yhbp_co_model_1.cif #5
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif
Chain information for fold_hqba_yhbp_co_model_2.cif #7
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif
Chain information for fold_hqba_yhbp_co_model_3.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif
Chain information for fold_hqba_yhbp_co_model_4.cif #9
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #4-5,7-9#!3,6 surfaces
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4-5,7-9 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8
RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
0.391)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_2.cif, chain A (#7), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.278 angstroms; (across all 167 pairs:
0.278)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_3.cif, chain A (#8), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.296 angstroms; (across all 167 pairs:
0.296)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
0.297)
> hide #!3 models
> show #!3 models
> hide #4 models
> show #4 models
> hide #!6 models
> hide #5 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #!3 models
> show #!6 models
> show #7 models
> hide #!6 models
> show #5 models
> show #8 models
> show #9 models
> color #4-5,7-9 bychain
> select clear
> hide #5 models
> hide #7 models
> show #5 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #5 models
> hide #4 models
> show #5 models
> show #7 models
> delete atoms #5,7-8
> delete bonds #5,7-8
> show #4 models
> show #9 models
> hide #9 models
> show #9 models
> hide #4 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
Chain information for fold_hqba_yhbp_co_model_1.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
> color #5,9 bychain
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #5 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)
> hide #9 models
> show #4 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
Chain information for fold_hqba_yhbq_co_model_0.cif #7
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif
Chain information for fold_hqba_yhbq_co_model_1.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif
Chain information for fold_hqba_yhbq_co_model_2.cif #10
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif
Chain information for fold_hqba_yhbq_co_model_3.cif #11
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif
Chain information for fold_hqba_yhbq_co_model_4.cif #12
---
Chain | Description
A | .
B | .
Computing secondary structure
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4-5,7-12 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8
RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
0.391)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_0.cif, chain A (#7), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
0.202)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_1.cif, chain A (#8), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.376 angstroms; (across all 167 pairs:
0.376)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
0.297)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)
> hide #4 models
> hide #5 models
> hide #8 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #8 models
> hide #7 models
> show #10 models
> hide #8 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> show #4 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #12 models
> show #12 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #12 models
> select clear
> show #7 models
> hide #7 models
> show #4 models
> hide #!6 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #5 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #7 models
> color #7#!3 bychain
> hide #7 models
> color #3 lime
> show #7 models
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #9 models
> hide #!3 models
> hide #7 models
> show #5 models
> hide #9 models
> show #9 models
> hide #5 models
> delete atoms #9
> delete bonds #9
> show #7 models
> show #!3 models
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #8 models
> show #10 models
> show #11 models
> show #12 models
> hide #7 models
> hide #!3 models
> show #4 models
> hide #8 models
> hide #10 models
> hide #12 models
> hide #11 models
> show #!6 models
> show #5 models
> hide #4 models
> hide #!6 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif
Chain information for fold_hqba_ubiu_model_0.cif #9
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif
Chain information for fold_hqba_ubiu_model_1.cif #13
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif
Chain information for fold_hqba_ubiu_model_2.cif #14
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif
Chain information for fold_hqba_ubiu_model_3.cif #15
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif
Chain information for fold_hqba_ubiu_model_4.cif #16
---
Chain | Description
A | .
B | .
Computing secondary structure
> show #!6 models
> hide #5 models
> hide #9 models
> ui tool show Matchmaker
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #9-16 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
0.273)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
0.260)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
0.235)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
0.229)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
0.219)
> show #9 models
> hide #!6 models
> show #!6 models
> hide #9 models
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> show #9 models
> hide #!6 models
> ui tool show Matchmaker
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> matchmaker #9-16 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
0.273)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
0.260)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
0.235)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
0.229)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
0.219)
> show #!6 models
> hide #!6 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> hide #9 models
> delete atoms #13-16
> delete bonds #13-16
> show #9 models
> color #9 bychain
> show #!6 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #9 models
> select clear
> select #6/A:164
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/A:23,24,27
24 atoms, 22 bonds, 3 residues, 1 model selected
> select #6/A:23,24,27,167
36 atoms, 34 bonds, 4 residues, 1 model selected
> color (#!6 & sel) cyan
> select clear
> show #9 models
> hide #!6 models
> show #7 models
> hide #9 models
> show #!6 models
> hide #!6 models
> show #8 models
> show #10 models
> show #11 models
> show #12 models
> hide #8 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #!6 models
> hide #7 models
> show #4 models
> show #5 models
> hide #!6 models
> hide #5 models
> show #5 models
> hide #4 models
> show #!6 models
> hide #5 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_0.cif
Chain information for fold_hqba_yhbq_model_0.cif #13
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_1.cif
Chain information for fold_hqba_yhbq_model_1.cif #14
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_2.cif
Chain information for fold_hqba_yhbq_model_2.cif #15
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_3.cif
Chain information for fold_hqba_yhbq_model_3.cif #16
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_4.cif
Chain information for fold_hqba_yhbq_model_4.cif #17
---
Chain | Description
A | .
B | .
Computing secondary structure
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #13-17 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
0.328)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
0.165)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
0.359)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
0.208)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)
> matchmaker #13-17 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
0.328)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
0.165)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
0.359)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
0.208)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)
> hide #!6 models
> show #7 models
> show #8 models
> hide #8 models
> show #8 models
> show #10 models
> show #11 models
> hide #11 models
> show #11 models
> show #12 models
> hide #!3 models
> hide #7 models
> hide #13 models
> delete atoms #8,10-12,14-17
> delete bonds #8,10-12,14-17
> show #4 models
> show #5 models
> hide #5 models
> show #7 models
> show #9 models
> hide #7 models
> hide #4 models
> show #13 models
> show #!6 models
> hide #!6 models
> show #4 models
> hide #9 models
> show #5 models
> hide #5 models
> hide #4 models
> show #!6 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #7 models
> hide #!6 models
> show #9 models
> hide #13 models
> hide #9 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_0.cif
Chain information for fold_hqba_ubiu_fe_model_0.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_1.cif
Chain information for fold_hqba_ubiu_fe_model_1.cif #10
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_2.cif
Chain information for fold_hqba_ubiu_fe_model_2.cif #11
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_3.cif
Chain information for fold_hqba_ubiu_fe_model_3.cif #12
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_4.cif
Chain information for fold_hqba_ubiu_fe_model_4.cif #14
---
Chain | Description
A | .
B | .
Computing secondary structure
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #8-14 to #6 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_fe_model_0.cif, chain A (#8), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.214 angstroms; (across all 167 pairs:
0.214)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
0.273)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_fe_model_1.cif, chain A (#10), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.234 angstroms; (across all 167 pairs:
0.234)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_fe_model_2.cif, chain A (#11), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.284 angstroms; (across all 167 pairs:
0.284)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_fe_model_3.cif, chain A (#12), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.300 angstroms; (across all 167 pairs:
0.300)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
0.328)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_fe_model_4.cif, chain A (#14), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.275 angstroms; (across all 167 pairs:
0.275)
> hide #8 models
> hide #7 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #14 models
> show #!6 models
> show #8 models
> hide #!6 models
> show #10 models
> hide #8 models
> show #12 models
> show #11 models
> hide #10 models
> hide #12 models
> show #8 models
> show #10 models
> show #12 models
> show #13 models
> show #14 models
> color #8,10-14 bychain
> hide #13 models
> hide #8 models
> hide #11 models
> hide #12 models
> hide #14 models
> show #11 models
> hide #10 models
> show #9 models
> hide #11 models
> show #8 models
> hide #9 models
> show #10 models
> hide #8 models
> show #11 models
> hide #10 models
> select #11/B:176
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B:193
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #11/B:176
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #11/B:232
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #11/B:169
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel yellow
> select clear
> show #12 models
> hide #11 models
> select add #12/B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12/B:176
12 atoms, 10 bonds, 2 residues, 1 model selected
> select clear
> show #14 models
> hide #12 models
> show #8 models
> show #9 models
> hide #14 models
> show #10 models
> hide #9 models
> select #10/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> select #8/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> hide #10 models
> show #9 models
> rainbow sel
> select clear
> hide #8 models
> show #10 models
> show #8 models
> hide #9 models
> hide #10 models
> show #9 models
> hide #9 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #14 models
> select #9/B#10/B#11/B#12/B#14/B
11805 atoms, 12065 bonds, 1500 residues, 5 models selected
> rainbow sel
> select clear
> hide #9 models
> hide #8 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #14 models
> show #9 models
> select #9/B:1-131
1030 atoms, 1053 bonds, 131 residues, 1 model selected
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> show #7 models
> show #9 models
> hide #7 models
> hide #8 models
> show #8 models
> hide #9 models
> show #10 models
> hide #8 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> show #14 models
> hide #12 models
> show #9 models
> show #8 models
> show #10 models
> show #11 models
> show #13 models
> hide #13 models
> show #12 models
> hide #14 models
> hide #12 models
> hide #11 models
> hide #10 models
> show #10 models
> show #11 models
> show #12 models
> show #14 models
> ui tool show Contacts
> contacts saveFile "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_UbiU_Fe.contacts.txt"
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #ed5ffc radius 0.06 reveal true
430 contacts
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #14 models
> show #2 models
> select #8/A:68,70,36,102,38,103,61
57 atoms, 53 bonds, 7 residues, 1 model selected
> select #8/A:68,70,36,102,38,103,61,37,67,105
86 atoms, 83 bonds, 10 residues, 1 model selected
> color sel magenta
> ui tool show "Color Actions"
> color sel thistle target acsp
> hide #2 models
> show #2 models
> hide #2 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> select clear
> select #8/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> color sel thistle target acsp
> select #8/A:68,70,36,102,38,103,61,37,67,105
86 atoms, 83 bonds, 10 residues, 1 model selected
> color sel medium purple target acsp
> select clear
> select #8/A:68,70,36,102,38,103,61,37,67,105
86 atoms, 83 bonds, 10 residues, 1 model selected
> color sel thistle target acsp
> select #8/A:68,70,36,102,38,103,61,37,67,105
86 atoms, 83 bonds, 10 residues, 1 model selected
> select #8/A:37
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:165,37,63,68,149,70,36,67,102,162,38,32,40,29,39,103,61,105
157 atoms, 150 bonds, 18 residues, 1 model selected
> color sel medium purple target acsp
> color sel pale violet red target acsp
> select #8/A:37,68,70,36,67,102,38,103,61,105
86 atoms, 83 bonds, 10 residues, 1 model selected
> color sel dark orchid target acsp
> select clear
> select #8/A:61
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/A:162
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #8/A:165
24 atoms, 22 bonds, 3 residues, 1 model selected
> show sel atoms
> select #8/A:62
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> show #9 models
> hide #8 models
> show #10 models
> hide #9 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> show #!6 models
> hide #12 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #12 models
> show #12#!3,6 surfaces
> hide #!3,6,12 surfaces
> hide #!12 models
> show #11 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #11 models
> hide #!6 models
> show #11 models
> show #!6 models
> hide #11 models
> hide #!6 models
> show #!6 models
> show #11 models
> hide #!6 models
> select #11/A#12/A
2622 atoms, 2682 bonds, 334 residues, 2 models selected
> show #!12 models
> ui tool show "Color Actions"
> color sel thistle target acsp
> select clear
> hide #!12 models
> select #11/B:193,232,169,176
24 atoms, 20 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark goldenrod target acsp
> color sel sienna target acsp
> select clear
> select #12/B:193,232,169,176
24 atoms, 20 bonds, 4 residues, 1 model selected
> show #!12 models
> hide #11 models
> hide #!3 models
> delete atoms (#!12 & sel)
> delete bonds (#!12 & sel)
> hide #!3 models
> select clear
> delete atoms #12
> delete bonds #12
> show #14 models
> select #14/B:193,232,169,176
24 atoms, 20 bonds, 4 residues, 1 model selected
> show #10 models
> hide #14 models
> select #10/B:193,232,169,176
24 atoms, 20 bonds, 4 residues, 1 model selected
> show #9 models
> hide #10 models
> show #8 models
> hide #9 models
> select #8/B:193,232,169,176
24 atoms, 20 bonds, 4 residues, 1 model selected
> hide #8 models
> show #8 models
> show #10 models
> hide #8 models
> show #14 models
> delete atoms #10,14
> delete bonds #10,14
> show #11 models
> show #!3 models
> color #3 #9ff996ff
> color #3 #b9f992ff
> color #3 #9af98eff
> color #3 #96f99cff
> color #3 #aef9bfff
> show #4 models
> hide #11 models
> show #!6 models
> hide #4 models
> show #11 models
> hide #!6 models
> select clear
> select #11/A:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #11/A:24
15 atoms, 13 bonds, 2 residues, 1 model selected
> show #!6 models
> hide #!6 models
> select add #11/A:27
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #11/A:167
36 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel cyan
> select clear
> show #!6 models
> hide #11 models
> show #11 models
> hide #!6 models
> show #!6 models
> hide #11 models
> show #2 models
> ui tool show Contacts
> hide #!3 models
> ui tool show Contacts
> contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/HqbA_Hfqx6.contacts.txt
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #fdd4f6 radius 0.06 reveal true
542 contacts
> hide #!6 models
> show #!3 models
> hide #2 models
> show #!3 cartoons
> select #3/A
1678 atoms, 1491 bonds, 404 residues, 1 model selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> ui tool show Contacts
> contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_CoA.4rs2.contact.txt
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #fdd4f6 radius 0.06 reveal true
668 contacts
> select ::name="HOH"
235 atoms, 112 pseudobonds, 235 residues, 2 models selected
> hide sel atoms
> show #2 models
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> select #3/B
1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> show sel atoms
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
1672 atoms, 1474 bonds, 668 pseudobonds, 418 residues, 2 models selected
> color sel gray target acsp
> color sel light gray target acsp
> select #3/B:74@SD
1 atom, 1 residue, 1 model selected
> color #2 white models
> color #2 #ffe0fcff models
> select #3/B:75
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show "Side View"
> select clear
> select #3/B:22,23,84,90,113,116,119,120
80 atoms, 76 bonds, 8 residues, 1 model selected
> color sel indian red target acsp
> color sel tomato target acsp
> select #3/B:24, 27, 167
26 atoms, 24 bonds, 3 residues, 1 model selected
> color sel coral target acsp
> color sel sienna target acsp
> color sel dark orange target acsp
> color sel goldenrod target acsp
> color sel peru target acsp
> color sel dark goldenrod target acsp
> select clear
> show #9 models
> hide #!3 models
> show #!3 models
> hide #9 models
> show #8 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #8 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #2 models
> hide #!6 models
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
1672 atoms, 1474 bonds, 668 pseudobonds, 418 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #!6 models
> show #2 models
> hide #!6 models
> show #!6 models
> select #3/B
1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected
> show sel cartoons
> hide #!6 models
> show sel atoms
> show #!6 models
> select #6/A:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium purple target acsp
> hide #!3 models
> color sel medium slate blue target acsp
> color sel medium purple target acsp
> color sel plum target acsp
> color sel thistle target acsp
> color sel lavender target acsp
> color sel medium slate blue target acsp
> select clear
> select #6/A:22,23,84,90,113,116,119,120
80 atoms, 76 bonds, 8 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel medium slate blue target acsp
> select clear
> show #!3 models
> select #3/B
1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
1672 atoms, 1474 bonds, 668 pseudobonds, 418 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #6/A:22,23,84,90,113,116,119,120
80 atoms, 76 bonds, 8 residues, 1 model selected
> color sel dark turquoise target acsp
> color sel spring green target acsp
> select clear
> show #11 models
> hide #!6 models
> select #11/A:22,23,84,90,113,116,119,120
80 atoms, 76 bonds, 8 residues, 1 model selected
> color sel lime target acsp
> select clear
> select #11/A:22,23,84,90,113,116,119,120
80 atoms, 76 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select #11/A:286,87,88
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #11/A:86,87,88
21 atoms, 20 bonds, 3 residues, 1 model selected
> show sel atoms
> show #!6 models
> hide #11 models
> select #3/B
1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected
> hide #!6 models
> show sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> show #!6 models
> show #11 models
> hide #!6 models
> select #11/A:86,87,88,77,21
35 atoms, 32 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel yellow green target acsp
> select #6/A:86,87,88,77,21
35 atoms, 32 bonds, 5 residues, 1 model selected
> show #!6 models
> hide #11 models
> show sel atoms
> color sel yellow green target acsp
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
> select #6/A:2,4,5,7,8,9,35,38,41,42,70,98,102,103,104,105
132 atoms, 126 bonds, 16 residues, 1 model selected
> show sel atoms
> color (#!6 & sel) magenta
> select clear
> show #11 models
> hide #!6 models
> select #11/A:32,36,37,38,61,67,68,70,102,103,105
96 atoms, 93 bonds, 11 residues, 1 model selected
> select #11/A:32,36,37,38,61,67,68,70,102,103,105,162,165
113 atoms, 108 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> color sel goldenrod target acsp
> color sel dark khaki target acsp
> color sel tan target acsp
> select clear
> show #7 models
> hide #11 models
> show #4 models
> hide #4 models
> show #4 models
> hide #7 models
> show #7 models
> hide #4 models
> ui tool show Contacts
> contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_YhbQ_Co.contacts.txt
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #fdd4f6 radius 0.06 reveal true
710 contacts
> ui tool show Contacts
> hide #!3 models
> ui tool show Contacts
> contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_YhbQ_Co.contacts.txt
> resSeparation 5 interModel false intraMol false ignoreHiddenModels true
> color #fdd4f6 radius 0.06 reveal true
42 contacts
> select #7/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple target acsp
> color sel plum target acsp
> color sel rosy brown target acsp
> color sel medium purple target acsp
> color sel medium orchid target acsp
> color sel medium slate blue target acsp
> color sel medium purple target acsp
> color sel thistle target acsp
> color sel medium purple target acsp
> color #7 #d97ae2ff
> color #7 #e291dcff
> color #7 #9f6ee2ff
> color #7 #bfade2ff
> color #7 #bc9de2ff
> color #7 #c7bce2ff
> color #7 #ccbde2ff
> color #7 #c6b0e2ff
> color #7 #bea9e2ff
> color #7 #ce9be2ff
> color #7 #d7b0e2ff
> color #7 #be92e2ff
> color #7 #ab8be2ff
> color #7 #e1bce2ff
> color #7 #c8aae2ff
> color #7 #c6a7e2ff
> color #7 #bf95e2ff
> color #7 #d18ee2ff
> color #7 #deaee2ff
> color #7 #e2aadfff
> color #7 #d3a1e2ff
> color #7 #d6b4e2ff
> color #7 #c5b4e2ff
> color #7 #bdafe2ff
> show #8 models
> hide #8 models
> select #7/B
795 atoms, 807 bonds, 100 residues, 1 model selected
> rainbow sel
> select clear
> select #7/C:1@CO
1 atom, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel medium aquamarine target acsp
> color sel cadet blue target acsp
> color sel medium turquoise target acsp
> color sel light sea green target acsp
> color sel cadet blue target acsp
> color sel medium sea green target acsp
> color sel cadet blue target acsp
> select clear
> select #7/A:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> select #7/A:2,4,5,7,32,94,98,102,103,144
94 atoms, 90 bonds, 10 residues, 1 model selected
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> ui tool show "Color Actions"
> color sel medium slate blue target acsp
> help help:user/tools/coloractions.html
> color sel purple target acsp
> select clear
> select #7/A:2,4,5,7,32,94,98,102,103,144
94 atoms, 90 bonds, 10 residues, 1 model selected
> show #11 models
> hide #7 models
> show #8 models
> hide #8 models
> show #!6 models
> hide #11 models
> show #7 models
> hide #!6 models
> show #4 models
> show #!6 models
> hide #!6 models
> hide #4 models
> show #!3 models
> hide #!3 models
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> show #7 atoms
> hide #7 atoms
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> show #7 atoms
> undo
> select #7/A:2,4,5,7,32,94,98,102,103,144
94 atoms, 90 bonds, 10 residues, 1 model selected
> show sel atoms
> select ::name="CO"
4 atoms, 4 residues, 4 models selected
> show sel & #7 atoms
> hide #2 models
> show #2 models
> ui tool show Contacts
> contacts resSeparation 5 interModel false intraMol false ignoreHiddenModels
> true color #fdd4f6 radius 0.06 reveal true
42 contacts
> show #!3 models
> hide #!3 models
> show #!3 models
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
1672 atoms, 1474 bonds, 9 pseudobonds, 418 residues, 2 models selected
> hide sel atoms
> select #7/A:86,87,88
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #7/A:86,87,88
21 atoms, 20 bonds, 3 residues, 1 model selected
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> select #7/A:24,27,167
27 atoms, 25 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel cyan
> select clear
> select #7/A:22,23,84,90,113,116,119,120
80 atoms, 76 bonds, 8 residues, 1 model selected
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> color sel lime target acsp
> select clear
> select #7/A:22,23,84,90,113,116,119,120
80 atoms, 76 bonds, 8 residues, 1 model selected
> show sel atoms
> show #!6 models
> hide #7 models
Drag select of 1 atoms, 6 residues, 1 bonds
> select clear
> show #7 models
> hide #!6 models
> select clear
> select #7/A:2,4,5,7,32,94,98,102,103,144
94 atoms, 90 bonds, 10 residues, 1 model selected
> color sel medium violet red target acsp
> color sel deep pink target acsp
> help help:user/tools/coloractions.html
> show #!6 models
> hide #7 models
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> hide sel atoms
> select #6/C:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select clear
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> color sel pale green target acsp
> color sel honeydew target acsp
> select clear
> show #7 models
> hide #!6 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #!3 models
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 33098 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" interactive
Using preset: Overall Look / Interactive
> set bgColor transparent
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> show #!5 models
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.cxs
opened ChimeraX session
> show #!6 models
> hide #7 models
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> select clear
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> hide #!3,6 surfaces
> show #7 models
> hide #!6 models
> select #7/B
795 atoms, 807 bonds, 100 residues, 1 model selected
> color sel light sky blue target acsp
> select clear
> select #7/B
795 atoms, 807 bonds, 100 residues, 1 model selected
> color sel powder blue target acsp
> select clear
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select clear
> select ::name="COA"
48 atoms, 50 bonds, 1 residue, 1 model selected
> style sel ball
Changed 48 atom styles
> select clear
> show #!6 models
> hide #7 models
> select clear
> select #6/A:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> select #6/A:103
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> undo
> select clear
> show #7 models
> hide #!6 models
> show #11 models
> show #!6 models
> hide #!6 models
> hide #7 models
> show #8 models
> hide #8 models
> select #1/B
688 atoms, 701 bonds, 87 residues, 1 model selected
> select #11/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> color sel khaki target acsp
> color sel wheat target acsp
> color sel beige target acsp
> color sel antique white target acsp
> select clear
> select #11/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> color sel pale goldenrod target acsp
> color sel light gray target acsp
> color sel burly wood target acsp
> color sel tan target acsp
> color sel navajo white target acsp
> color sel beige target acsp
> color sel wheat target acsp
> color sel beige target acsp
> color sel antique white target acsp
> select clear
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting soft
> show #!6 models
> hide #11 models
> lighting full
> lighting soft
> lighting simple
> show #11 models
> hide #!6 models
> select #11/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> color sel wheat target acsp
> select clear
> select #11/A:32,36,37,38,61,67,68,70,102,103,105,162,165
113 atoms, 108 bonds, 13 residues, 1 model selected
> color sel dark orange target acsp
> select clear
> select #11/B165
Nothing selected
> select #11/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> hide sel atoms
> select clear
> show #8 models
> hide #8 models
> select #11/B:176
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B:232,169,176,193
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel yellow
> select clear
> show #8 models
> hide #11 models
> show #11 models
> hide #8 models
> show #9 models
> hide #9 models
> show #7 models
> hide #11 models
> show #!6 models
> hide #7 models
> show #8 models
> hide #!6 models
> show #11 models
> hide #8 models
> show #!6 models
> show #7 models
> hide #!6 models
> hide #11 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> show #11 models
> hide #!6 models
> hide #7 models
> show #!6 models
> show #7 models
> hide #11 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> select ::name="CO"
4 atoms, 4 residues, 4 models selected
> show sel & #!6 atoms
> ui tool show "Color Actions"
> color sel light steel blue target acsp
> color sel silver target acsp
> color sel dark blue target acsp
> select clear
> select ::name="CO"
4 atoms, 4 residues, 4 models selected
> color sel medium blue target acsp
> select clear
> select #6/A:144
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel deep sky blue target acsp
> color sel royal blue target acsp
> select clear
> show #7 models
> hide #!6 models
> select #7/A:32
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel royal blue target acsp
> select clear
> show #!6 models
> hide #7 models
> select clear
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> hide #!6 models
> show #!6 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #11 models
> hide #7 models
> show #!6 models
> show #7 models
> hide #7 models
> hide #!6 models
> show #!6 models
> hide #11 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_Hfq_Co.png
> width 900 height 668 supersample 4 transparentBackground true
> show #7 models
> hide #!6 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_YhbQ_Co.png
> width 900 height 668 supersample 4 transparentBackground true
> show #11 models
> hide #7 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_UbiU_Co.png
> width 900 height 668 supersample 4 transparentBackground true
> select #11/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!3,11 surfaces
> select clear
> select #11/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> show #!6 models
> hide #!11 models
> show #7 models
> hide #!6 models
> show #!11 models
> hide #7 models
> select #11/A:33
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #11/A:39
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add #11/A:66
23 atoms, 21 bonds, 3 residues, 2 models selected
> select #11/A:62
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/A:63
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #11/A:39
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add #11/A:33
27 atoms, 25 bonds, 3 residues, 2 models selected
> hide sel atoms
> select #11/A:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!6 models
> hide #!11 models
> show #!11 models
> hide #!6 models
> show #!6 models
> hide #!11 models
> show #!11 models
> hide #!6 models
> select #11/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!3,11 surfaces
> show #!6 models
> hide #!11 models
> show #!11 models
> hide #!6 models
> show #!6 models
> hide #!11 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!6 models
> show #7 models
> show #!11 models
> hide #7 models
> select #11/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> select clear
> show #!6 models
> hide #!11 models
> transparency #2-3,6 30
> transparency #2-3,6 10
> select clear
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!6 models
> hide #!3,11 surfaces
> select #11/C:1@FE
1 atom, 1 residue, 1 model selected
> select #11/B
2361 atoms, 2413 bonds, 300 residues, 1 model selected
> rainbow sel
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_UbiU_Fe.rainbow.png
> width 900 height 668 supersample 4 transparentBackground true
> show #7 models
> hide #!11 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
opened ChimeraX session
> show #1 models
> hide #!13 models
> show #!2 models
> hide #!2 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
> show #!2 models
> hide #!3 models
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> show #!3 models
> hide #!2 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!19 models
> hide #1 models
> show #1 models
> select #19/B
2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected
> rainbow sel
> hide #1 models
> show #1 models
> hide #!19 models
> show #!19 models
> hide #1 models
> show #1 models
> hide #!19 models
> show #!19 models
> hide #1 models
> select #19/A
2063 atoms, 1951 bonds, 4 pseudobonds, 400 residues, 2 models selected
> hide sel cartoons
> select clear
> show #1 models
> hide #!19 models
> show #!18 models
> show #!17 models
> hide #!18 models
> show #!19 models
> hide #!17 models
> hide #1 models
> show #1 models
> hide #!19 models
> show #!19 models
> show #1#!19 cartoons
> hide #!19 models
> show #!19 models
> hide #1 models
> select #19
4091 atoms, 3902 bonds, 8 pseudobonds, 765 residues, 2 models selected
> color sel bychain
> show #1 models
> select clear
> select #1/A:169
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> hide #1 models
> select #2/A:169
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="FAD"
583 atoms, 638 bonds, 11 residues, 7 models selected
> ui tool show "Color Actions"
> color sel wheat target acsp
> select clear
> show #1 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:10
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:18-19
14 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/A:26
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:26
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:19
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #19/B
Alignment identifier is 19/B
> select #19/B:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #19/B:15
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #19/B:17
26 atoms, 24 bonds, 3 residues, 1 model selected
> select add #19/B:18
34 atoms, 31 bonds, 4 residues, 1 model selected
> select #1/A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:24-27
33 atoms, 33 bonds, 4 residues, 1 model selected
> select #19/B:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/B:15-18
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #1/A:194
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 12 residues
> select clear
> select #19/B:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/B:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/B:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_4.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_4.cif
Chain information for fold_azor_monomer_fad_model_0.cif #22
---
Chain | Description
A | .
Chain information for fold_azor_monomer_fad_model_1.cif #23
---
Chain | Description
A | .
Chain information for fold_azor_monomer_fad_model_2.cif #24
---
Chain | Description
A | .
Chain information for fold_azor_monomer_fad_model_3.cif #25
---
Chain | Description
A | .
Chain information for fold_azor_monomer_fad_model_4.cif #26
---
Chain | Description
A | .
Chain information for fold_azor_monomer_model_1.cif #27
---
Chain | Description
A | .
Chain information for fold_azor_monomer_model_2.cif #28
---
Chain | Description
A | .
Chain information for fold_azor_monomer_model_3.cif #29
---
Chain | Description
A | .
Chain information for fold_azor_monomer_model_4.cif #30
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #22-30 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#22), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_1.cif, chain A (#23), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_2.cif, chain A (#24), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.447 angstroms; (across all 208 pairs:
0.447)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_3.cif, chain A (#25), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.420 angstroms; (across all 208 pairs:
0.420)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_4.cif, chain A (#26), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.291 angstroms; (across all 208 pairs:
0.291)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_1.cif, chain A (#27), sequence alignment score =
1086.8
RMSD between 208 pruned atom pairs is 0.117 angstroms; (across all 208 pairs:
0.117)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_2.cif, chain A (#28), sequence alignment score =
1086.8
RMSD between 208 pruned atom pairs is 0.103 angstroms; (across all 208 pairs:
0.103)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_3.cif, chain A (#29), sequence alignment score =
1086.8
RMSD between 208 pruned atom pairs is 0.129 angstroms; (across all 208 pairs:
0.129)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_4.cif, chain A (#30), sequence alignment score =
1086.8
RMSD between 208 pruned atom pairs is 0.121 angstroms; (across all 208 pairs:
0.121)
> hide #!19 models
> hide #23 models
> hide #22 models
> hide #24 models
> hide #25 models
> hide #26 models
> hide #1 models
> delete atoms #27-30
> delete bonds #27-30
> show #1 models
> show #22 models
> show #23 models
> show #24 models
> show #25 models
> show #26 models
> select ::name="FAD"
848 atoms, 928 bonds, 16 residues, 12 models selected
> color sel gray target acsp
> select clear
> hide #22 models
> hide #1 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> delete atoms #23-26
> delete bonds #23-26
> show #22 models
> show #1 models
> select #1/A:12
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #1 models
> select #22/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select clear
> select #1/A:16
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:16-19
27 atoms, 26 bonds, 4 residues, 1 model selected
> show #1 models
> show sel atoms
> hide #1 models
> show #!19 models
> hide #!19 models
> show #!19 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
Log from Wed Mar 11 15:25:43 2026UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
Log from Wed Feb 18 08:19:31 2026UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsDx2.af3_contacts.cxs
Log from Mon Jun 24 12:21:56 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
> format session
Log from Thu Jun 20 17:06:26 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
> format session
Log from Thu Jun 20 14:21:45 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsD.AF3vsAF2.cxs
Log from Thu Jun 20 13:37:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Wed May 22 02:35:17 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/taic/Desktop/Smf1MrkD_model0.cxs
Log from Wed May 22 02:14:18 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
2024-05-22 01:52:01,857 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("<urllib3.connection.HTTPConnection object at
0x30b3499d0>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8]
nodename nor servname provided, or not known)")':
/cxservices/api/v1/chimerax/updates?uuid=76645f75-4e6d-5780-8383-9cae5a361a94&OS=macosx&OSVersion=14.4.1&ChimeraXVersion=1.7.1
2024-05-22 01:52:01,859 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("<urllib3.connection.HTTPConnection object at
0x30b3480d0>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8]
nodename nor servname provided, or not known)")':
/cxservices/api/v1/chimerax/updates?uuid=76645f75-4e6d-5780-8383-9cae5a361a94&OS=macosx&OSVersion=14.4.1&ChimeraXVersion=1.7.1
2024-05-22 01:52:01,863 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NameResolutionError("<urllib3.connection.HTTPConnection object at
0x30b34b490>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8]
nodename nor servname provided, or not known)")':
/cxservices/api/v1/chimerax/updates?uuid=76645f75-4e6d-5780-8383-9cae5a361a94&OS=macosx&OSVersion=14.4.1&ChimeraXVersion=1.7.1
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_0.cif
Chain information for fold_smf1_mrkd_model_0.cif #1
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_4.cif
Chain information for fold_smf1_mrkd_model_4.cif #2
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_1.cif
Chain information for fold_smf1_mrkd_model_1.cif #3
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_2.cif
Chain information for fold_smf1_mrkd_model_2.cif #4
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_3.cif
Chain information for fold_smf1_mrkd_model_3.cif #5
---
Chain | Description
A | .
B | .
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> select /B:1-344
12720 atoms, 12915 bonds, 1720 residues, 5 models selected
> select /B:1-344
12720 atoms, 12915 bonds, 1720 residues, 5 models selected
> select /B:1-344
12720 atoms, 12915 bonds, 1720 residues, 5 models selected
> select /A:1-179
6440 atoms, 6545 bonds, 895 residues, 5 models selected
> select /B:1-344
12720 atoms, 12915 bonds, 1720 residues, 5 models selected
> color (#1 & sel) blue
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select clear
[Repeated 1 time(s)]
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> select /A:1-179
6440 atoms, 6545 bonds, 895 residues, 5 models selected
> color (#1 & sel) hot pink
> ui tool show "Color Actions"
> color sel tomato
> color sel light salmon
> color sel hot pink
> select clear
Drag select of 3 residues
> select clear
[Repeated 1 time(s)]
> select /B:1-344
12720 atoms, 12915 bonds, 1720 residues, 5 models selected
> color (#1 & sel) cornflower blue
> select clear
Drag select of 5 residues
> select clear
[Repeated 1 time(s)]
> save /Users/taic/Desktop/Smf1MrkD_model0.cxs
——— End of log from Wed May 22 02:14:18 2024 ———
opened ChimeraX session
> select add #2
3832 atoms, 3892 bonds, 523 residues, 1 model selected
> select add #3
7664 atoms, 7784 bonds, 1046 residues, 2 models selected
> select add #4
11496 atoms, 11676 bonds, 1569 residues, 3 models selected
> select add #5
15328 atoms, 15568 bonds, 2092 residues, 4 models selected
> select add #1
19160 atoms, 19460 bonds, 2615 residues, 5 models selected
> select subtract #1
15328 atoms, 15568 bonds, 2092 residues, 4 models selected
> hide #1 target a
> show #5 models
> hide #5 models
> show #5 models
> delete atoms (#5 & sel)
> delete bonds (#5 & sel)
> show #4 models
> delete atoms (#4 & sel)
> delete bonds (#4 & sel)
> show #2 models
> delete atoms (#2 & sel)
> delete bonds (#2 & sel)
> show #3 models
> delete atoms sel
> delete bonds sel
> select 24-33
Expected an objects specifier or a keyword
> select .24-33
Expected an objects specifier or a keyword
> select /A:24
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A24-33
Nothing selected
> select /A:24-33
72 atoms, 72 bonds, 10 residues, 1 model selected
> color sel magenta
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> save /Users/taic/Desktop/Smf1MrkD_model0.cxs
——— End of log from Wed May 22 02:35:17 2024 ———
opened ChimeraX session
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/Smf1_MrkD.af3.pdb
> relModel #1
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_4.cif
Chain information for fold_smf1_mrkd_model_1.cif #2
---
Chain | Description
A | .
B | .
Chain information for fold_smf1_mrkd_model_2.cif #3
---
Chain | Description
A | .
B | .
Chain information for fold_smf1_mrkd_model_3.cif #4
---
Chain | Description
A | .
B | .
Chain information for fold_smf1_mrkd_model_4.cif #5
---
Chain | Description
A | .
B | .
> toolshed show
> select add #1
3832 atoms, 3892 bonds, 523 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #3-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_smf1_mrkd_model_2.cif, chain B (#3), sequence alignment score = 1735.3
RMSD between 300 pruned atom pairs is 0.511 angstroms; (across all 344 pairs:
4.630)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_smf1_mrkd_model_3.cif, chain B (#4), sequence alignment score = 1735.3
RMSD between 297 pruned atom pairs is 0.704 angstroms; (across all 344 pairs:
6.718)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_smf1_mrkd_model_4.cif, chain B (#5), sequence alignment score = 1735.3
RMSD between 300 pruned atom pairs is 0.417 angstroms; (across all 344 pairs:
4.893)
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> select clear
> show #2 models
> toolshed show
> ui tool show Matchmaker
> select /A
6440 atoms, 6545 bonds, 895 residues, 5 models selected
> hide #2 models
> select /B
12720 atoms, 12915 bonds, 1720 residues, 5 models selected
> show #2 models
> matchmaker #2-5 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_smf1_mrkd_model_1.cif, chain B (#2), sequence alignment score = 1726.3
RMSD between 298 pruned atom pairs is 0.483 angstroms; (across all 344 pairs:
3.904)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_smf1_mrkd_model_2.cif, chain B (#3), sequence alignment score = 1735.3
RMSD between 300 pruned atom pairs is 0.511 angstroms; (across all 344 pairs:
4.630)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_smf1_mrkd_model_3.cif, chain B (#4), sequence alignment score = 1735.3
RMSD between 297 pruned atom pairs is 0.704 angstroms; (across all 344 pairs:
6.718)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_smf1_mrkd_model_4.cif, chain B (#5), sequence alignment score = 1735.3
RMSD between 300 pruned atom pairs is 0.417 angstroms; (across all 344 pairs:
4.893)
> select clear
> show #3 models
> hide #2 models
Drag select of 32 residues
Drag select of 26 residues
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> show #2 models
> show #3 models
> show #4 models
> select add #1
4031 atoms, 3892 bonds, 550 residues, 2 models selected
> select subtract #1
199 atoms, 27 residues, 1 model selected
> select add #2
4031 atoms, 3892 bonds, 550 residues, 2 models selected
> select add #3
7664 atoms, 7784 bonds, 1046 residues, 2 models selected
> select add #4
11496 atoms, 11676 bonds, 1569 residues, 3 models selected
> select add #5
15328 atoms, 15568 bonds, 2092 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_4.cif
Chain information for fold_mrkd_model_0.cif #2
---
Chain | Description
A | .
Chain information for fold_mrkd_model_1.cif #3
---
Chain | Description
A | .
Chain information for fold_mrkd_model_2.cif #4
---
Chain | Description
A | .
Chain information for fold_mrkd_model_3.cif #5
---
Chain | Description
A | .
Chain information for fold_mrkd_model_4.cif #6
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #3-6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_1.cif,
chain A (#3), sequence alignment score = 1734.1
RMSD between 301 pruned atom pairs is 0.546 angstroms; (across all 344 pairs:
5.711)
Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_2.cif,
chain A (#4), sequence alignment score = 1680.1
RMSD between 308 pruned atom pairs is 0.938 angstroms; (across all 344 pairs:
3.574)
Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_3.cif,
chain A (#5), sequence alignment score = 1705.3
RMSD between 316 pruned atom pairs is 0.705 angstroms; (across all 344 pairs:
2.935)
Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_4.cif,
chain A (#6), sequence alignment score = 1737.1
RMSD between 300 pruned atom pairs is 0.954 angstroms; (across all 344 pairs:
2.984)
> hide #1 models
> hide #3 models
> show #3 models
> hide #2 models
> show #2 models
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3
2544 atoms, 2583 bonds, 344 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select add #3
2544 atoms, 2583 bonds, 344 residues, 1 model selected
> select add #4
5088 atoms, 5166 bonds, 688 residues, 2 models selected
> select add #5
7632 atoms, 7749 bonds, 1032 residues, 3 models selected
> select add #6
10176 atoms, 10332 bonds, 1376 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #1 models
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_mrkd_model_0.cif, chain A (#2), sequence alignment score = 1629.1
RMSD between 170 pruned atom pairs is 0.392 angstroms; (across all 344 pairs:
10.184)
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/af3.MrkD_Smf1.cxs
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_4.cif
Chain information for fold_smf1_model_0.cif #3
---
Chain | Description
A | .
Chain information for fold_smf1_model_1.cif #4
---
Chain | Description
A | .
Chain information for fold_smf1_model_2.cif #5
---
Chain | Description
A | .
Chain information for fold_smf1_model_3.cif #6
---
Chain | Description
A | .
Chain information for fold_smf1_model_4.cif #7
---
Chain | Description
A | .
> hide #1 models
> hide #2 models
> ui tool show Matchmaker
> matchmaker #4-7 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_1.cif,
chain A (#4), sequence alignment score = 874.3
RMSD between 151 pruned atom pairs is 0.152 angstroms; (across all 179 pairs:
4.075)
Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_2.cif,
chain A (#5), sequence alignment score = 874.3
RMSD between 167 pruned atom pairs is 0.473 angstroms; (across all 179 pairs:
1.868)
Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_3.cif,
chain A (#6), sequence alignment score = 874.3
RMSD between 141 pruned atom pairs is 0.157 angstroms; (across all 179 pairs:
6.954)
Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_4.cif,
chain A (#7), sequence alignment score = 874.3
RMSD between 149 pruned atom pairs is 0.191 angstroms; (across all 179 pairs:
5.505)
> select clear
[Repeated 1 time(s)]
> select add #4
1288 atoms, 1309 bonds, 179 residues, 1 model selected
> select add #5
2576 atoms, 2618 bonds, 358 residues, 2 models selected
> select add #6
3864 atoms, 3927 bonds, 537 residues, 3 models selected
> select add #7
5152 atoms, 5236 bonds, 716 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> select #1/A
1288 atoms, 1309 bonds, 179 residues, 1 model selected
> show #1 models
> hide #3 models
> matchmaker #3 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_smf1_mrkd_model_0.cif, chain A (#1) with
fold_smf1_model_0.cif, chain A (#3), sequence alignment score = 847.3
RMSD between 146 pruned atom pairs is 0.267 angstroms; (across all 179 pairs:
7.118)
> show #3 models
> hide #1 models
> select clear
> show #1 models
> hide #1 models
> show #1 models
> select #1/A:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:33
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:32
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> show #3 models
> show #1 models
> hide #1 models
> hide #3 models
> show #1 models
Drag select of 2 residues
[Repeated 1 time(s)]Drag select of 5 residues
> select clear
> select #1/B:197
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:197
14 atoms, 14 bonds, 2 residues, 2 models selected
> style sel stick
Changed 14 atom styles
> show sel cartoons
> show sel atoms
> select clear
[Repeated 1 time(s)]
> hide #1-2 atoms
> select #1/B:197
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:197
14 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
[Repeated 1 time(s)]
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_4.cif
Chain information for fold_mrkd_smf1x2_model_0.cif #4
---
Chain | Description
A | .
B C | .
Chain information for fold_mrkd_smf1x2_model_1.cif #5
---
Chain | Description
A | .
B C | .
Chain information for fold_mrkd_smf1x2_model_2.cif #6
---
Chain | Description
A | .
B C | .
Chain information for fold_mrkd_smf1x2_model_3.cif #7
---
Chain | Description
A | .
B C | .
Chain information for fold_mrkd_smf1x2_model_4.cif #8
---
Chain | Description
A | .
B C | .
> hide #2 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_MarkD_Smf1.cxs
> ui tool show Matchmaker
> matchmaker #4-8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_mrkd_smf1x2_model_0.cif, chain A (#4), sequence alignment score = 1735.3
RMSD between 317 pruned atom pairs is 0.717 angstroms; (across all 344 pairs:
1.803)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_mrkd_smf1x2_model_1.cif, chain A (#5), sequence alignment score = 1735.3
RMSD between 317 pruned atom pairs is 0.658 angstroms; (across all 344 pairs:
2.621)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_mrkd_smf1x2_model_2.cif, chain A (#6), sequence alignment score = 1735.3
RMSD between 323 pruned atom pairs is 0.662 angstroms; (across all 344 pairs:
1.119)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_mrkd_smf1x2_model_3.cif, chain A (#7), sequence alignment score = 1726.3
RMSD between 326 pruned atom pairs is 0.578 angstroms; (across all 344 pairs:
1.658)
Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
fold_mrkd_smf1x2_model_4.cif, chain A (#8), sequence alignment score = 1735.3
RMSD between 320 pruned atom pairs is 0.580 angstroms; (across all 344 pairs:
2.113)
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_MarkD_Smf1.cxs
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> show #4 models
> hide #1 models
> show #1 models
> hide #1 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #2 models
> hide #2 models
> show #1 models
> hide #1 models
Drag select of 50 residues
> select add #4
5409 atoms, 5201 bonds, 741 residues, 5 models selected
> select subtract #4
289 atoms, 39 residues, 4 models selected
> select add #5
5328 atoms, 5201 bonds, 730 residues, 4 models selected
> select add #6
10376 atoms, 10402 bonds, 1422 residues, 4 models selected
> select add #7
15415 atoms, 15603 bonds, 2113 residues, 4 models selected
> select add #8
20480 atoms, 20804 bonds, 2808 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_4.cif
Chain information for fold_mrkd_smf1x2_chaperone_model_0.cif #5
---
Chain | Description
A | .
B C | .
D | .
Chain information for fold_mrkd_smf1x2_chaperone_model_1.cif #6
---
Chain | Description
A | .
B C | .
D | .
Chain information for fold_mrkd_smf1x2_chaperone_model_2.cif #7
---
Chain | Description
A | .
B C | .
D | .
Chain information for fold_mrkd_smf1x2_chaperone_model_3.cif #8
---
Chain | Description
A | .
B C | .
D | .
Chain information for fold_mrkd_smf1x2_chaperone_model_4.cif #9
---
Chain | Description
A | .
B C | .
D | .
> ui tool show Matchmaker
> matchmaker #5-9 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5), sequence alignment score
= 1684.9
RMSD between 174 pruned atom pairs is 0.454 angstroms; (across all 344 pairs:
13.892)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_1.cif, chain A (#6), sequence alignment score
= 1690.3
RMSD between 170 pruned atom pairs is 0.422 angstroms; (across all 344 pairs:
13.078)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_2.cif, chain A (#7), sequence alignment score
= 1679.5
RMSD between 162 pruned atom pairs is 0.341 angstroms; (across all 344 pairs:
14.032)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_3.cif, chain A (#8), sequence alignment score
= 1688.5
RMSD between 171 pruned atom pairs is 0.409 angstroms; (across all 344 pairs:
14.387)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_4.cif, chain A (#9), sequence alignment score
= 1670.5
RMSD between 167 pruned atom pairs is 0.440 angstroms; (across all 344 pairs:
13.538)
> hide #4 models
> ui tool show Matchmaker
> matchmaker #6-9 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
fold_mrkd_smf1x2_chaperone_model_1.cif, chain A (#6), sequence alignment score
= 1705.9
RMSD between 285 pruned atom pairs is 1.036 angstroms; (across all 344 pairs:
3.694)
Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
fold_mrkd_smf1x2_chaperone_model_2.cif, chain A (#7), sequence alignment score
= 1714.9
RMSD between 142 pruned atom pairs is 0.412 angstroms; (across all 344 pairs:
7.789)
Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
fold_mrkd_smf1x2_chaperone_model_3.cif, chain A (#8), sequence alignment score
= 1723.9
RMSD between 321 pruned atom pairs is 0.448 angstroms; (across all 344 pairs:
2.302)
Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
fold_mrkd_smf1x2_chaperone_model_4.cif, chain A (#9), sequence alignment score
= 1705.9
RMSD between 300 pruned atom pairs is 0.999 angstroms; (across all 344 pairs:
4.300)
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> show #4 models
> hide #5 models
> show #1 models
> hide #1 models
> select #4/A
2544 atoms, 2583 bonds, 344 residues, 1 model selected
> matchmaker #5-9 to #4 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5), sequence alignment score
= 1684.9
RMSD between 174 pruned atom pairs is 0.454 angstroms; (across all 344 pairs:
13.892)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_1.cif, chain A (#6), sequence alignment score
= 1690.3
RMSD between 170 pruned atom pairs is 0.422 angstroms; (across all 344 pairs:
13.078)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_2.cif, chain A (#7), sequence alignment score
= 1679.5
RMSD between 162 pruned atom pairs is 0.341 angstroms; (across all 344 pairs:
14.032)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_3.cif, chain A (#8), sequence alignment score
= 1688.5
RMSD between 171 pruned atom pairs is 0.409 angstroms; (across all 344 pairs:
14.387)
Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
fold_mrkd_smf1x2_chaperone_model_4.cif, chain A (#9), sequence alignment score
= 1670.5
RMSD between 167 pruned atom pairs is 0.440 angstroms; (across all 344 pairs:
13.538)
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> hide #9 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> show #5 models
> hide #4 models
> show #6 models
> select #5/D
1844 atoms, 1886 bonds, 242 residues, 1 model selected
> rainbow sel
> hide #5 models
> hide #6 models
> show #5 models
> select add #5
6964 atoms, 7087 bonds, 944 residues, 1 model selected
> rainbow sel
> select clear
> color #5 bychain
> show #6 models
> hide #5 models
> color #6 bychain
> show #5 models
> hide #5 models
> show #7 models
> hide #6 models
> color #7 bychain
> show #8 models
> hide #7 models
> color #8 bychain
> show #9 models
> hide #8 models
> color #9 bychain
> show #8 models
> show #7 models
> show #6 models
> show #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> hide #6 models
> hide #7 models
> hide #9 models
> hide #8 models
> show #1 models
> hide #5 models
> show #4 models
> hide #1 models
> select #5/A
2544 atoms, 2583 bonds, 344 residues, 1 model selected
> select #4/A
2544 atoms, 2583 bonds, 344 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select #4/B
1288 atoms, 1309 bonds, 179 residues, 1 model selected
> color sel hot pink
> select #4/B:24
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:24-33
501 atoms, 502 bonds, 70 residues, 7 models selected
> color sel magenta
> select /C:24-33
432 atoms, 432 bonds, 60 residues, 6 models selected
> color sel forest green
> color sel lime green
> color sel sea green
> select #4/A:306
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:24-33
432 atoms, 432 bonds, 60 residues, 6 models selected
> color sel magenta
> color sel green
> select clear
> select add #3
1288 atoms, 1309 bonds, 179 residues, 1 model selected
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/Smf1.af3.pdb
> models #3
> select subtract #3
Nothing selected
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/MrkD.af3.pdb
> models #2
> hide #4 models
> show #2 models
> show #3 models
> hide #2 models
> show #1 models
> hide #3 models
> show #4 models
> hide #1 models
> show #5 models
> hide #4 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smlt_rs03360chaperone/fold_smlt_rs03360chaperone_model_0.cif
Chain information for fold_smlt_rs03360chaperone_model_0.cif #10
---
Chain | Description
A | .
> hide #5 models
> show #5 models
> hide #10 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_MarkD_Smf1.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_4.cif
Chain information for fold_igaa_rcsf_model_0.cif #1
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsf_model_1.cif #2
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsf_model_2.cif #3
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsf_model_3.cif #4
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsf_model_4.cif #5
---
Chain | Description
A | .
B | .
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_1.cif, chain A (#2), sequence alignment score = 3685.9
RMSD between 521 pruned atom pairs is 0.855 angstroms; (across all 711 pairs:
4.046)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_2.cif, chain A (#3), sequence alignment score = 3684.1
RMSD between 476 pruned atom pairs is 1.001 angstroms; (across all 711 pairs:
4.084)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_3.cif, chain A (#4), sequence alignment score = 3674.5
RMSD between 588 pruned atom pairs is 0.972 angstroms; (across all 711 pairs:
2.309)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_4.cif, chain A (#5), sequence alignment score = 3630.7
RMSD between 513 pruned atom pairs is 0.831 angstroms; (across all 711 pairs:
7.825)
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/af2.3.1/IgaA_RcsF.full/IgaA_RcsF.full.ranked_0.pdb
[Repeated 1 time(s)]Cannot open files: [Errno 60] Operation timed out
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/af2.3.1/IgaA_RcsF.full/IgaA_RcsF.full.ranked_0.pdb
Cannot open files: [Errno 60] Operation timed out
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.full.af2.pdb
Chain information for IgaA_RcsF.full.af2.pdb #6
---
Chain | Description
A | No description available
B | No description available
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 3610.6
RMSD between 211 pruned atom pairs is 0.633 angstroms; (across all 711 pairs:
11.108)
> select #1/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> matchmaker #2-6 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678
RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
23.597)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678
RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
21.352)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678
RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
6.659)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8
RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
14.431)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678
RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
22.199)
> select #6/A
11187 atoms, 11321 bonds, 711 residues, 1 model selected
> color sel blue
> select #6/B
2000 atoms, 2017 bonds, 134 residues, 1 model selected
> color sel red
> select clear
> select /B
6920 atoms, 7022 bonds, 804 residues, 6 models selected
> matchmaker #2-6 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678
RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
23.597)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678
RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
21.352)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678
RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
6.659)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8
RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
14.431)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678
RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
22.199)
> matchmaker #2-6 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678
RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
23.597)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678
RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
21.352)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678
RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
6.659)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8
RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
14.431)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678
RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
22.199)
> matchmaker #2-6 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678
RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
23.597)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678
RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
21.352)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678
RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
6.659)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8
RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
14.431)
Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678
RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
22.199)
> select /A
39202 atoms, 40006 bonds, 4266 residues, 6 models selected
> matchmaker #2-6 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_1.cif, chain A (#2), sequence alignment score = 3685.9
RMSD between 521 pruned atom pairs is 0.855 angstroms; (across all 711 pairs:
4.046)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_2.cif, chain A (#3), sequence alignment score = 3684.1
RMSD between 476 pruned atom pairs is 1.001 angstroms; (across all 711 pairs:
4.084)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_3.cif, chain A (#4), sequence alignment score = 3674.5
RMSD between 588 pruned atom pairs is 0.972 angstroms; (across all 711 pairs:
2.309)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_4.cif, chain A (#5), sequence alignment score = 3630.7
RMSD between 513 pruned atom pairs is 0.831 angstroms; (across all 711 pairs:
7.825)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 3610.6
RMSD between 211 pruned atom pairs is 0.633 angstroms; (across all 711 pairs:
11.108)
> select #1/A:508
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #3 models
> hide #4 models
> hide #5 models
> hide #2 models
> select add #2
6596 atoms, 6746 bonds, 846 residues, 2 models selected
> show #2 models
> rainbow sel
> hide #1 models
> hide #6 models
> select clear
> select #2/A:645
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/A:711
10 atoms, 9 bonds, 1 residue, 1 model selected
> select subtract #2/A:711
Nothing selected
> select /A:375-711
18203 atoms, 18527 bonds, 2022 residues, 6 models selected
> matchmaker #2-6 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_1.cif, chain A (#2), sequence alignment score = 1758.2
RMSD between 321 pruned atom pairs is 0.760 angstroms; (across all 337 pairs:
1.922)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_2.cif, chain A (#3), sequence alignment score = 1754.6
RMSD between 322 pruned atom pairs is 0.682 angstroms; (across all 337 pairs:
2.315)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_3.cif, chain A (#4), sequence alignment score = 1754.6
RMSD between 312 pruned atom pairs is 0.735 angstroms; (across all 337 pairs:
2.317)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_4.cif, chain A (#5), sequence alignment score = 1751
RMSD between 320 pruned atom pairs is 0.672 angstroms; (across all 337 pairs:
2.072)
Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1742
RMSD between 221 pruned atom pairs is 0.564 angstroms; (across all 337 pairs:
7.369)
> show #1 models
> show #6 models
> select clear
> hide #6 models
> hide #2 models
> show #2 models
> hide #1 models
> select add #3
6587 atoms, 6738 bonds, 845 residues, 1 model selected
> select add #4
13174 atoms, 13476 bonds, 1690 residues, 2 models selected
> select add #5
19761 atoms, 20214 bonds, 2535 residues, 3 models selected
> select add #1
26348 atoms, 26952 bonds, 3380 residues, 4 models selected
> select add #2
32935 atoms, 33690 bonds, 4225 residues, 5 models selected
> rainbow sel & #2
[Repeated 1 time(s)]
> show #1 models
> select subtract #1
26348 atoms, 26952 bonds, 3380 residues, 4 models selected
> select subtract #2
19761 atoms, 20214 bonds, 2535 residues, 3 models selected
> select subtract #3
13174 atoms, 13476 bonds, 1690 residues, 2 models selected
> select add #3
19761 atoms, 20214 bonds, 2535 residues, 3 models selected
> select subtract #4
13174 atoms, 13476 bonds, 1690 residues, 2 models selected
> select subtract #3
6587 atoms, 6738 bonds, 845 residues, 1 model selected
> select subtract #5
Nothing selected
> select clear
> hide #2 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #6 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.AF3vs2.cxs
> show #2 models
> hide #1 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.AF3vs2.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_4.cif
Chain information for fold_igaa_rcsd_model_0.cif #1
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsd_model_1.cif #2
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsd_model_2.cif #3
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsd_model_3.cif #4
---
Chain | Description
A | .
B | .
Chain information for fold_igaa_rcsd_model_4.cif #5
---
Chain | Description
A | .
B | .
> ui tool show Matchmaker
> select /A:375-711
13020 atoms, 13290 bonds, 1685 residues, 5 models selected
No reference and/or match structure/chain chosen
> matchmaker #2-5 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsd_model_1.cif, chain A (#2), sequence alignment score = 1746.2
RMSD between 325 pruned atom pairs is 0.852 angstroms; (across all 337 pairs:
1.129)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsd_model_2.cif, chain A (#3), sequence alignment score = 1737.2
RMSD between 248 pruned atom pairs is 0.910 angstroms; (across all 337 pairs:
2.172)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsd_model_3.cif, chain A (#4), sequence alignment score = 1746.2
RMSD between 327 pruned atom pairs is 0.857 angstroms; (across all 337 pairs:
1.514)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsd_model_4.cif, chain A (#5), sequence alignment score = 1754
RMSD between 286 pruned atom pairs is 0.647 angstroms; (across all 337 pairs:
3.056)
> hide #2 models
> show #2 models
> hide #3 models
> hide #4 models
> show #4 models
> show #3 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> show #2 models
> select add #1
23077 atoms, 23545 bonds, 2949 residues, 5 models selected
> select add #2
33134 atoms, 33800 bonds, 4213 residues, 5 models selected
> select subtract #1
20473 atoms, 20887 bonds, 2612 residues, 4 models selected
> hide #1 models
> rainbow sel & #2
> select clear
> show #1 models
> hide #2 models
> select add #1
12661 atoms, 12913 bonds, 1601 residues, 1 model selected
> color sel bychain
> show #2 models
> hide #1 models
> select subtract #1
Nothing selected
> show #1 models
> hide #1 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.full.af2.pdb
Chain information for IgaA_RcsF.full.af2.pdb #6
---
Chain | Description
A | No description available
B | No description available
> select add #6
13187 atoms, 13338 bonds, 845 residues, 1 model selected
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/IgaA_RcsF.full.af2.pdb
Chain information for IgaA_RcsF.full.af2.pdb #7
---
Chain | Description
A | No description available
B | No description available
> select add #7
26374 atoms, 26676 bonds, 1690 residues, 2 models selected
> select subtract #6
13187 atoms, 13338 bonds, 845 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/IgaA_RcsD.dm.af2.pdb
Chain information for IgaA_RcsD.dm.af2.pdb #7
---
Chain | Description
A | No description available
B | No description available
> hide #6 models
> select /A:375-711
18203 atoms, 18527 bonds, 2022 residues, 6 models selected
> matchmaker #6-7 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1730
RMSD between 165 pruned atom pairs is 0.793 angstroms; (across all 337 pairs:
8.672)
> matchmaker #6-7 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1730
RMSD between 165 pruned atom pairs is 0.793 angstroms; (across all 337 pairs:
8.672)
> hide #2 models
No reference and/or match structure/chain chosen
> matchmaker #7 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with IgaA_RcsD.dm.af2.pdb,
chain A (#7), sequence alignment score = 1470.3
RMSD between 143 pruned atom pairs is 0.843 angstroms; (across all 285 pairs:
3.900)
> show #1 models
> show #6 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_0.cif
Chain information for fold_igaa_rcsf_model_0.cif #8
---
Chain | Description
A | .
B | .
> hide #6 models
> hide #7 models
> select /A:375-711
20807 atoms, 21185 bonds, 2359 residues, 7 models selected
> matchmaker #8 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_0.cif, chain A (#8), sequence alignment score = 1746.2
RMSD between 164 pruned atom pairs is 0.791 angstroms; (across all 337 pairs:
7.310)
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/IgaA_RcsD.AF3vsAF2.cxs
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsD.AF3vsAF2.cxs
——— End of log from Thu Jun 20 13:37:04 2024 ———
opened ChimeraX session
> hide #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #8 models
> select add #8
24790 atoms, 25265 bonds, 2867 residues, 7 models selected
> select add #1
34847 atoms, 35520 bonds, 4131 residues, 7 models selected
> select subtract #1
22186 atoms, 22607 bonds, 2530 residues, 6 models selected
> select subtract #8
15599 atoms, 15869 bonds, 1685 residues, 5 models selected
> select add #6
23603 atoms, 23970 bonds, 2193 residues, 5 models selected
> select subtract #6
10416 atoms, 10632 bonds, 1348 residues, 4 models selected
> select add #2
20473 atoms, 20887 bonds, 2612 residues, 4 models selected
> select add #3
30530 atoms, 31142 bonds, 3876 residues, 4 models selected
> select add #4
40587 atoms, 41397 bonds, 5140 residues, 4 models selected
> select add #5
50644 atoms, 51652 bonds, 6404 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #1 models
> show #6 models
> hide #1 models
> show #1 models
> show #8 models
> show #7 models
> ui tool show Matchmaker
> select /A:375-711
10391 atoms, 10553 bonds, 1011 residues, 3 models selected
> hide #1 models
> hide #7 models
> hide #8 models
> show #7 models
> hide #6 models
> show #6 models
> matchmaker #6-8 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1730
RMSD between 165 pruned atom pairs is 0.793 angstroms; (across all 337 pairs:
8.672)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with IgaA_RcsD.dm.af2.pdb,
chain A (#7), sequence alignment score = 1470.3
RMSD between 143 pruned atom pairs is 0.843 angstroms; (across all 285 pairs:
3.900)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsf_model_0.cif, chain A (#8), sequence alignment score = 1746.2
RMSD between 164 pruned atom pairs is 0.791 angstroms; (across all 337 pairs:
7.310)
> show #1 models
> show #8 models
> hide #1 models
> hide #8 models
> select /A
26974 atoms, 27426 bonds, 2434 residues, 4 models selected
> ui tool show "Color Actions"
> color sel gold
> color sel goldenrod
> show #1 models
> hide #6 models
> hide #7 models
> show #6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #7 models
> hide #6 models
> show #6 models
> show #8 models
> hide #7 models
> select #6/B
2000 atoms, 2017 bonds, 134 residues, 1 model selected
> color sel navy
> color sel medium purple
> select clear
> select #8/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> color sel dark orchid
> select clear
> select #8/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> color sel orange
> color sel gold
> select clear
> show #7 models
> hide #8 models
> show #1 models
> hide #6 models
> show #8 models
> hide #7 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsD.AF3vsAF2.cxs
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_4.cif
Chain information for fold_igaa_rcsf_rcsdx2_model_0.cif #2
---
Chain | Description
A | .
B | .
C D | .
Chain information for fold_igaa_rcsf_rcsdx2_model_1.cif #3
---
Chain | Description
A | .
B | .
C D | .
Chain information for fold_igaa_rcsf_rcsdx2_model_2.cif #4
---
Chain | Description
A | .
B | .
C D | .
Chain information for fold_igaa_rcsf_rcsdx2_model_3.cif #5
---
Chain | Description
A | .
B | .
C D | .
Chain information for fold_igaa_rcsf_rcsdx2_model_4.cif #9
---
Chain | Description
A | .
B | .
C D | .
> hide #1 models
> hide #8 models
> ui tool show Matchmaker
> select /A:375-711
23411 atoms, 23843 bonds, 2696 residues, 8 models selected
> matchmaker #2-5,9 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsf_rcsdx2_model_0.cif, chain A (#2), sequence alignment score =
1750.4
RMSD between 220 pruned atom pairs is 1.035 angstroms; (across all 337 pairs:
10.315)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsf_rcsdx2_model_1.cif, chain A (#3), sequence alignment score =
1742.6
RMSD between 235 pruned atom pairs is 1.120 angstroms; (across all 337 pairs:
5.345)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsf_rcsdx2_model_2.cif, chain A (#4), sequence alignment score =
1754
RMSD between 160 pruned atom pairs is 0.743 angstroms; (across all 337 pairs:
8.032)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsf_rcsdx2_model_3.cif, chain A (#5), sequence alignment score =
1746.2
RMSD between 228 pruned atom pairs is 1.069 angstroms; (across all 337 pairs:
9.420)
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
fold_igaa_rcsf_rcsdx2_model_4.cif, chain A (#9), sequence alignment score =
1750.4
RMSD between 231 pruned atom pairs is 1.149 angstroms; (across all 337 pairs:
9.284)
> show #1 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #9 models
> hide #1 models
> select add #2
41510 atoms, 42275 bonds, 4984 residues, 8 models selected
> select add #1
51567 atoms, 52530 bonds, 6248 residues, 8 models selected
> select add #3
69666 atoms, 70962 bonds, 8536 residues, 8 models selected
> select add #4
87765 atoms, 89394 bonds, 10824 residues, 8 models selected
> select subtract #1
75104 atoms, 76481 bonds, 9223 residues, 7 models selected
> select subtract #3
54401 atoms, 55391 bonds, 6598 residues, 6 models selected
> select subtract #4
33698 atoms, 34301 bonds, 3973 residues, 5 models selected
> select add #5
51797 atoms, 52733 bonds, 6261 residues, 5 models selected
> select add #6
59801 atoms, 60834 bonds, 6769 residues, 5 models selected
> select subtract #5
39098 atoms, 39744 bonds, 4144 residues, 4 models selected
> select subtract #6
25911 atoms, 26406 bonds, 3299 residues, 3 models selected
> select add #8
29894 atoms, 30486 bonds, 3807 residues, 3 models selected
> select add #9
47993 atoms, 48918 bonds, 6095 residues, 3 models selected
> select subtract #8
41406 atoms, 42180 bonds, 5250 residues, 2 models selected
> select subtract #9
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> color sel bychain
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #3 models
> hide #2 models
> show #2 models
> hide #2 models
> select add #3
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> select add #4
41406 atoms, 42180 bonds, 5250 residues, 2 models selected
> select add #5
62109 atoms, 63270 bonds, 7875 residues, 3 models selected
> select add #9
82812 atoms, 84360 bonds, 10500 residues, 4 models selected
> color sel & #3 bychain
> select clear
> show #2 models
> show #4 models
> hide #3 models
> hide #2 models
> select add #4
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> color sel bychain
> show #5 models
> hide #4 models
> select add #5
41406 atoms, 42180 bonds, 5250 residues, 2 models selected
> select subtract #4
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> color sel bychain
> show #9 models
> select add #9
41406 atoms, 42180 bonds, 5250 residues, 2 models selected
> hide #5 models
> select subtract #5
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> color sel bychain
> select clear
> show #2 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaAfull_RcsF_RcsDdimer.af2.pdb
Chain information for IgaAfull_RcsF_RcsDdimer.af2.pdb #10
---
Chain | Description
A | No description available
B | No description available
C D | No description available
> hide #2 models
> hide #9 models
> matchmaker #10 to #1 & sel
No 'to' model specified
> select /A:375-711
28594 atoms, 29080 bonds, 3033 residues, 9 models selected
> matchmaker #10 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
IgaAfull_RcsF_RcsDdimer.af2.pdb, chain A (#10), sequence alignment score =
1733.6
RMSD between 185 pruned atom pairs is 0.860 angstroms; (across all 337 pairs:
7.525)
> show #1 models
> hide #1 models
> select add #10
45158 atoms, 45835 bonds, 4083 residues, 9 models selected
> color sel & #10 bychain
> show #2 models
> hide #10 models
> show #6 models
> hide #6 models
> show #6 models
> show #7 models
> hide #7 models
> hide #6 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> select #1/B
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> color sel medium aquamarine
> select clear
> show #2 models
> show #8 models
> hide #1 models
> hide #2 models
> show #1 models
> show #2 models
> hide #1 models
> hide #2 models
> show #10 models
> hide #8 models
> show #2 models
> show #1 models
> hide #2 models
> hide #10 models
> show #8 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
——— End of log from Thu Jun 20 14:21:45 2024 ———
opened ChimeraX session
> show #2 models
> hide #1 models
> hide #8 models
Drag select of 16 residues
> select add #2/C:223
121 atoms, 3 bonds, 17 residues, 1 model selected
Drag select of 8 residues
> select add #2/C:187
190 atoms, 10 bonds, 26 residues, 1 model selected
> select add #2/C:196
201 atoms, 20 bonds, 27 residues, 1 model selected
> select add #2/C:197
210 atoms, 28 bonds, 28 residues, 1 model selected
> ui tool show Contacts
> select #2/C:224
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:225
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:60
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #2/B:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:225
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:60
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:59
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:538
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:540
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:224
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/C:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:222
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/B:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 20 residues
> select /D:411
35 atoms, 30 bonds, 5 residues, 5 models selected
> select #2/D:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select /C:411
35 atoms, 30 bonds, 5 residues, 5 models selected
> show sel & #2 atoms
> select #2/A:98
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:98
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #2/A:97
23 atoms, 22 bonds, 2 residues, 1 model selected
> select add #2/A:96
30 atoms, 28 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> select #2/C:413
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/C:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /:94
Expected an objects specifier or a keyword
> select /A:94
70 atoms, 60 bonds, 10 residues, 10 models selected
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:98
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:99
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:101
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #2/A:102
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:104
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #2
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> surface sel
> transparency (#!2 & sel) 70
> select subtract #2
4 models selected
> hide #!2 models
> show #!2 models
> surface hidePatches #2
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select add #2
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> surface (#!2 & sel)
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
——— End of log from Thu Jun 20 17:06:26 2024 ———
opened ChimeraX session
> select add #9
41406 atoms, 42180 bonds, 5250 residues, 2 models selected
> select add #2
41406 atoms, 42180 bonds, 5250 residues, 2 models selected
> select subtract #2
20703 atoms, 21090 bonds, 2625 residues, 1 model selected
> hide #!2 models
> show #9 models
> show #5 models
> select add #5
41406 atoms, 42180 bonds, 5250 residues, 2 models selected
> show #4 models
> select add #4
62109 atoms, 63270 bonds, 7875 residues, 3 models selected
> show #3 models
> select add #3
82812 atoms, 84360 bonds, 10500 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #!2 models
> show #!2 models
> hide #!2 surfaces
> show #6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #6 models
> show #6 models
> hide #6 models
> show #8 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #10 models
> hide #8 models
> hide #!2 models
> show #1 models
> select clear
> ui tool show Contacts
> contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_Rcsf_RcsDx2.af3_contacts.txt
> interModel false intraMol false reveal true
1756 contacts
Drag select of 5 residues
Drag select of 42 residues
> hide #10 models
> select clear
> show #!2 models
> hide #1 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsDx2.af3_contacts.cxs
[Repeated 1 time(s)]
——— End of log from Mon Jun 24 12:21:56 2024 ———
opened ChimeraX session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_0.cif
Chain information for fold_rcsdx2_model_0.cif #4
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_1.cif
Chain information for fold_rcsdx2_model_1.cif #5
---
Chain | Description
A B | .
Computing secondary structure
[Repeated 1 time(s)]
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_2.cif
Chain information for fold_rcsdx2_model_2.cif #9
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_3.cif
Chain information for fold_rcsdx2_model_3.cif #11
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_4.cif
Chain information for fold_rcsdx2_model_4.cif #12
---
Chain | Description
A B | .
Computing secondary structure
> hide #!2 models
> hide #3 models
> hide #4 models
> show #4 models
> hide #5 models
> hide #9 models
> hide #11 models
> hide #12 models
> color #4 bychain
> show #5 models
> hide #4 models
> hide #5 models
> show #4 models
> show #!2 models
> hide #4 models
> show #12 models
> hide #!2 models
> show #11 models
> select add #11
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> select add #12
28232 atoms, 28704 bonds, 3560 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> show #5 models
> select add #5
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #9 models
> select add #9
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #4 models
> hide #4 models
> show #!2 models
> hide #!2 models
> show #1 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_1.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_2.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_3.json
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_4.json
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_0.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_0.cif #5
---
Chain | Description
A | .
B C | .
D E | .
> hide #1,5 surfaces
[Repeated 1 time(s)]
> show #1,5 cartoons
Computing secondary structure
> hide #1,5 surfaces
> select add #5
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> style sel stick
Changed 34679 atom styles
> hide sel atoms
> select clear
> hide #1 models
> color #5 bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_1.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_1.cif #9
---
Chain | Description
A | .
B C | .
D E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_4.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_4.cif #11
---
Chain | Description
A | .
B C | .
D E | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_2.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_2.cif #12
---
Chain | Description
A | .
B C | .
D E | .
> show #5,9,11-12 cartoons
Computing secondary structure
[Repeated 2 time(s)]
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_3.cif
Chain information for fold_igaa_rcscx2_rcsdx2_model_3.cif #13
---
Chain | Description
A | .
B C | .
D E | .
> hide #5,9,11-13 atoms
> hide #5 models
> hide #9 models
> show #9 models
> hide #11 models
> hide #12 models
> hide #13 models
> color #9 bychain
> show #11 models
> hide #9 models
> color #11 bychain
> show #12 models
> hide #11 models
> color #12 bychain
> select add #12
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #13 models
> select add #13
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> show #11 models
> hide #13 models
> select subtract #13
Nothing selected
> show #13 models
> hide #11 models
> select add #13
34679 atoms, 35323 bonds, 4389 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #11 models
> show #9 models
> show #10 models
> hide #9 models
> hide #11 models
> show #11 models
> hide #10 models
> show #!2 models
> hide #11 models
> show #10 models
> hide #!2 models
> show #9 models
> hide #10 models
> show #1 models
> show #!2 models
> hide #1 models
> hide #9 models
> show #9 models
> hide #!2 models
> show #4 models
> hide #9 models
> select add #4
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #7 models
> show #8 models
> hide #8 models
> hide #7 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_0.cif
Chain information for fold_rcsdx2_rcscx2_model_0.cif #4
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> color #4 bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_1.cif
Chain information for fold_rcsdx2_rcscx2_model_1.cif #12
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_3.cif
Chain information for fold_rcsdx2_rcscx2_model_3.cif #13
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_4.cif
Chain information for fold_rcsdx2_rcscx2_model_4.cif #14
---
Chain | Description
A B | .
C D | .
Computing secondary structure
[Repeated 2 time(s)]
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_2.cif
Chain information for fold_rcsdx2_rcscx2_model_2.cif #15
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #4 models
> hide #13 models
> hide #14 models
> hide #15 models
> color #12 bychain
> hide #12 models
> show #13 models
> color #13 bychain
> show #14 models
> hide #13 models
> color #14 bychain
> show #15 models
> hide #14 models
> color #15 bychain
> show #14 models
> hide #15 models
> show #4 models
> hide #14 models
> show #12 models
> hide #12 models
> show #12 models
> hide #4 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> hide #15 models
> show #15 models
> show #4 models
> hide #15 models
> show #12 models
> hide #4 models
> show #9 models
> hide #12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/D
Alignment identifier is 9/D
> select
> #9/D:91-96,99-103,110-114,144-148,155-159,197-199,203-205,210-219,227-234,248-252,270-274,278-285,290-297,367-372,377-381,407-412,415-423,430-437,525-528,550-555,562-565,589-596,603-610,657-663,667-675,695-699,719-721,734-737,747-751,757-761,764-768
1522 atoms, 1520 bonds, 183 residues, 1 model selected
> hide #9 models
> show #7 models
> show #1 models
> hide #7 models
> color #1 bychain
> select
> #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
selected
> rainbow sel & #1
> select clear
> show #4 models
> hide #4 models
> select
> #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
selected
> ui tool show Matchmaker
> matchmaker #4-15#!2 & sel to #1 & sel
Computing secondary structure
[Repeated 7 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
chain B (#7), sequence alignment score = 1372.7
RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
1.791)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
4552.2
RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
23.121)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
1374.5
RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
1.531)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
4504.2
RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
19.956)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
4506.6
RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
45.059)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
4461.6
RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
37.620)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
4539.6
RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
22.279)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
4538.4
RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
33.986)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
4543.2
RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
51.173)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
4535.4
RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
25.202)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
4532.4
RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
32.264)
> matchmaker #4-15#!2 & sel to #1 & sel
Computing secondary structure
[Repeated 7 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
chain B (#7), sequence alignment score = 1372.7
RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
1.791)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
4552.2
RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
23.121)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
1374.5
RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
1.531)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
4504.2
RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
19.956)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
4506.6
RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
45.059)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
4461.6
RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
37.620)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
4539.6
RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
22.279)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
4538.4
RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
33.986)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
4543.2
RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
51.173)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
4535.4
RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
25.202)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
4532.4
RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
32.264)
> matchmaker #4-15#!2 & sel to #1 & sel
Computing secondary structure
[Repeated 7 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
chain B (#7), sequence alignment score = 1372.7
RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
1.791)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
4552.2
RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
23.121)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
1374.5
RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
1.531)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
4504.2
RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
19.956)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
4506.6
RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
45.059)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
4461.6
RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
37.620)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
4539.6
RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
22.279)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
4538.4
RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
33.986)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
4543.2
RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
51.173)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
4535.4
RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
25.202)
Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
4532.4
RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
32.264)
> show #!2 models
> hide #1 models
> show #1 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> select
> #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
selected
> rainbow sel
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> select clear
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #1 models
> show #4 models
> hide #!2 models
> show #5 models
> hide #4 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> show #5 models
> hide #9 models
> show #9 models
> hide #9 models
> show #10 models
> hide #5 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #!2 models
> hide #15 models
> show #5 models
> hide #!2 models
> show #12 models
> hide #5 models
> show #13 models
> hide #12 models
> hide #13 models
> show #14 models
> show #15 models
> hide #14 models
> show #!2 models
> hide #15 models
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> color #!2 bychain
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> select ~sel & ##selected
15100 atoms, 15353 bonds, 1028 pseudobonds, 1914 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> show sel cartoons
> select ~sel & ##selected
19719 atoms, 20089 bonds, 1028 pseudobonds, 2491 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> rainbow sel
> hide sel cartoons
> select #2/C/D
14116 atoms, 14352 bonds, 638 pseudobonds, 1780 residues, 2 models selected
> show sel cartoons
> rainbow sel
> select clear
> hide #!2 cartoons
[Repeated 1 time(s)]
> show #!2 cartoons
> color #!2 bychain
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> color sel bychain
> select clear
> color #!2 bychain
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> rainbow sel
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> rainbow sel
> select clear
> show #9 models
> hide #!2 models
> show #!2 models
> hide #9 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_3.cif
Chain information for fold_rcsdx2_rcsbx2_model_3.cif #16
---
Chain | Description
A B | .
C D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_4.cif
Chain information for fold_rcsdx2_rcsbx2_model_4.cif #17
---
Chain | Description
A B | .
C D | .
Computing secondary structure
[Repeated 1 time(s)]
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_0.cif
Chain information for fold_rcsdx2_rcsbx2_model_0.cif #18
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #!2 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_1.cif
Chain information for fold_rcsdx2_rcsbx2_model_1.cif #19
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_2.cif
Chain information for fold_rcsdx2_rcsbx2_model_2.cif #20
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> hide #16 models
> hide #17 models
> hide #19 models
> hide #20 models
> color #18 bychain
> show #19 models
> hide #18 models
> color #19 bychain
> show #20 models
> hide #19 models
> color #20 bychain
> show #17 models
> hide #20 models
> color #17 bychain
> show #1 models
> hide #17 models
> show #4 models
> hide #1 models
> show #1 models
> hide #1 models
> color #4 bychain
> select #4/B
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> select #4/C
7480 atoms, 7617 bonds, 949 residues, 1 model selected
> rainbow sel
> select clear
> select #4/A/B/C
21596 atoms, 21969 bonds, 2729 residues, 1 model selected
> hide sel cartoons
> undo
> select #4/A/B/D
21596 atoms, 21969 bonds, 2729 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> color #4 bychain
> select #4/A
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> rainbow sel
> select clear
> select #4/B/C/D
22018 atoms, 22410 bonds, 2788 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #4/D
7480 atoms, 7617 bonds, 949 residues, 1 model selected
> rainbow sel
> select clear
> select #4/D
7480 atoms, 7617 bonds, 949 residues, 1 model selected
> select clear
> hide #4 models
> show #1 models
> color #1 bychain
> select #1/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #8 models
> hide #1 models
Drag select of 12 residues
Drag select of 1 residues
> show #3 models
Drag select of 3 atoms, 5 residues
> select #8/A:472
8 atoms, 7 bonds, 1 residue, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 69358 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #3 models
> show #4 models
> hide #8 models
> select #4/A/B
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> rainbow sel
> select clear
> color #4 bychain
> select #4/A/B
14116 atoms, 14352 bonds, 1780 residues, 1 model selected
> rainbow sel
> select clear
[Repeated 1 time(s)]
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> color #4,12-15 bychain
> select #4/A/B#12/A/B#13/A/B#14/A/B#15/A/B
70580 atoms, 71760 bonds, 8900 residues, 5 models selected
> rainbow sel
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> select clear
> hide #4 models
> show #12 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #15 models
> color #5 bychain
> select #5/B/C
14960 atoms, 15234 bonds, 1898 residues, 1 model selected
> rainbow sel
> select clear
> hide #5 models
> show #4 models
> show #!2 models
> hide #4 models
Drag select of 18 residues
> show #4 models
> hide #!2 models
> show #12 models
> hide #4 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> hide #15 models
> show #12 models
> show #4 models
> hide #12 models
> show #13 models
> hide #4 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #12 models
> hide #15 models
> show #!2 models
> hide #12 models
Drag select of 6 residues
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #2 magenta
> undo
> select #2/C:412
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) magenta
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #3 models
> select #2/C:412
8 atoms, 7 bonds, 1 residue, 1 model selected
> rainbow sel
> select #2/C:410
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> rainbow sel
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!2 & sel) magenta
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!2 & sel) yellow
> ui tool show "Color Actions"
> color sel green yellow
> select clear
> select #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel yellow
> select clear
> select #2/C:413
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/C:414
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!2 & sel) cornflower blue
> select add #2/C:413
13 atoms, 11 bonds, 2 residues, 2 models selected
> select add #2/C:414
21 atoms, 18 bonds, 3 residues, 3 models selected
> color (#!2 & sel) yellow
> select clear
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select clear
[Repeated 2 time(s)]
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> rainbow sel
> select clear
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> color sel bychain
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light steel blue
> select #2/B
984 atoms, 1001 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel burly wood
> color sel rosy brown
> color sel tan
> color sel dark salmon
> color sel peru
> color sel dark goldenrod
> select #2/C
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> color sel light slate gray
> select clear
> select #2/D
7058 atoms, 7176 bonds, 890 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light steel blue
> select clear
Drag select of 4 residues
> select clear
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/A:96
12 atoms, 10 bonds, 2 residues, 2 models selected
> select subtract #2/A:96
5 atoms, 4 bonds, 1 residue, 2 models selected
> select add #2/A:96
12 atoms, 10 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cyan
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> undo
[Repeated 2 time(s)]
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/A:94
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> color sel gray
> color sel silver
> color sel dark gray
> select clear
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:94
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/A:94
16 atoms, 14 bonds, 2 residues, 2 models selected
> color sel deep sky blue
> select add #2/C:411
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #2/C:413
31 atoms, 27 bonds, 4 residues, 3 models selected
> select add #2/C:414
39 atoms, 34 bonds, 5 residues, 3 models selected
> color sel plum
> color sel pale violet red
> color sel magenta
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/A:94
16 atoms, 14 bonds, 2 residues, 2 models selected
> color sel deep sky blue
> select clear
> select add #2/C:411
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/C:413
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #2/C:414
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #2/A:97
34 atoms, 30 bonds, 4 residues, 2 models selected
> select add #2/A:94
39 atoms, 34 bonds, 5 residues, 3 models selected
> label (#!2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 1
> select clear
[Repeated 1 time(s)]
> hide #3 models
> show #3 models
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
---
note | Fetching CCD CO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CO/CO.cif
Chain information for fold_hqba_yhbq_co_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif
Chain information for fold_hqba_yhbq_co_model_1.cif #2
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif
Chain information for fold_hqba_yhbq_co_model_2.cif #3
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif
Chain information for fold_hqba_yhbq_co_model_3.cif #4
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif
Chain information for fold_hqba_yhbq_co_model_4.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 3 time(s)]
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif
Chain information for fold_hqba_yhbp_co_model_0.cif #6
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
Chain information for fold_hqba_yhbp_co_model_1.cif #7
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif
Chain information for fold_hqba_yhbp_co_model_2.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif
Chain information for fold_hqba_yhbp_co_model_3.cif #9
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif
Chain information for fold_hqba_yhbp_co_model_4.cif #10
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 4 time(s)]
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif
Chain information for fold_hqba_ubiu_model_0.cif #11
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif
Chain information for fold_hqba_ubiu_model_1.cif #12
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif
Chain information for fold_hqba_ubiu_model_2.cif #13
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif
Chain information for fold_hqba_ubiu_model_3.cif #14
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif
Chain information for fold_hqba_ubiu_model_4.cif #15
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 4 time(s)]
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif
---
note | Fetching CCD FE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif
Chain information for fold_hqba_nfua_fe4_co_model_0.cif #16
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_1.cif
Chain information for fold_hqba_nfua_fe4_co_model_1.cif #17
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_2.cif
Chain information for fold_hqba_nfua_fe4_co_model_2.cif #18
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_3.cif
Chain information for fold_hqba_nfua_fe4_co_model_3.cif #19
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_4.cif
Chain information for fold_hqba_nfua_fe4_co_model_4.cif #20
---
Chain | Description
A | .
B | .
Computing secondary structure
[Repeated 4 time(s)]
> color bychain
> select /AA
Nothing selected
> select /A
26220 atoms, 26820 bonds, 3340 residues, 20 models selected
> ui tool show Matchmaker
> matchmaker #2-20 to #1 & sel
Computing secondary structure
[Repeated 19 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
0.416)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
0.283)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
0.340)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
0.303)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4
RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
0.452)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4
RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
0.507)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
0.304)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
0.350)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
0.343)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
0.286)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
0.302)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
0.276)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
0.268)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
0.331)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
0.226)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
871.4
RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
0.589)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
0.390)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
849.8
RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
0.211)
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> open 4RS2 fromDatabase pdb format mmcif
Summary of feedback from opening 4RS2 fetched from pdb
---
notes | Fetching compressed mmCIF 4rs2 from http://files.rcsb.org/download/4rs2.cif
Fetching CCD COA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/COA/COA.cif
4rs2 title:
1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
Escherichia coli in Complex with CoA [more info...]
Chain information for 4rs2 #21
---
Chain | Description | UniProt
A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167
Non-standard residues in 4rs2 #21
---
COA — coenzyme A
4rs2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /A
27898 atoms, 28311 bonds, 3744 residues, 21 models selected
> ui tool show Matchmaker
> matchmaker #21 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
(#21), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> select clear
> select #21/A
1678 atoms, 1491 bonds, 404 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 8 8 GLN B 8 GLU B 18 1 11
Start residue of secondary structure not found: HELIX 9 9 LYS B 56 ALA B 58 1
3
Start residue of secondary structure not found: HELIX 10 10 GLN C 8 GLU C 18 1
11
Start residue of secondary structure not found: HELIX 11 11 LYS C 56 ALA C 58
1 3
Start residue of secondary structure not found: HELIX 12 12 SER C 72 ASN C 74
1 3
39 messages similar to the above omitted
Chain information for Hfq6_YhbS.af2.4rs2.pdb
---
Chain | Description
22.1/A | No description available
22.2/A | No description available
22.1/B 22.1/C 22.1/D 22.1/E 22.1/F 22.1/G | No description available
22.2/B | No description available
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #1-5,21#!22.1-2 atoms
> hide #!22.2 models
> show #!22.2 models
> hide #!22.1 models
> show #!22.1 models
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!22.2 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> hide #21 models
> show #21 models
> ui tool show Matchmaker
> matchmaker #!22.1-2 to #1 & sel
Computing secondary structure
[Repeated 2 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
Hfq6_YhbS.af2.4rs2.pdb, chain A (#22.1), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> hide #21 models
> show #21 models
> hide #21 models
> show #21 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #21 models
> select add #22
16588 atoms, 16330 bonds, 40 pseudobonds, 1769 residues, 6 models selected
> delete atoms (#!22.1-2 & sel)
> delete bonds (#!22.1-2 & sel)
> show #21 models
> select add #21
4709 atoms, 4356 bonds, 990 residues, 3 models selected
> select subtract #21
1311 atoms, 1341 bonds, 167 residues, 2 models selected
> hide #22 models
> hide #21 models
> select subtract #22
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show #22 models
> select add #22
1311 atoms, 1341 bonds, 167 residues, 2 models selected
> select add #1
2107 atoms, 2148 bonds, 268 residues, 2 models selected
> select subtract #1
1 model selected
> show #1 models
> hide #1 models
> delete atoms #22
> delete bonds #22
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/AF2-multi/Hfq6mer_YhbS/YhbS-
> Hfq6mer.ranked_0.pdb
Chain information for YhbS-Hfq6mer.ranked_0.pdb #23
---
Chain | Description
A | No description available
B C D E F G | No description available
> hide #23 atoms
> show #23 cartoons
Computing secondary structure
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2-21,23 to #1 & sel
Computing secondary structure
[Repeated 21 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
0.416)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
0.283)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
0.340)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
0.303)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4
RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
0.452)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4
RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
0.507)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
0.304)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
0.350)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
0.343)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
0.286)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
0.302)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4
RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
0.276)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
0.268)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
0.331)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
0.226)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
871.4
RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
0.589)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
871.4
RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
0.390)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
849.8
RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
0.211)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
(#21), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
> hide #22 models
> show #1 models
> hide #1 models
> select #23/B
1552 atoms, 1566 bonds, 102 residues, 1 model selected
> Sel #23/B/C/D/E/F/G
Unknown command: Sel #23/B/C/D/E/F/G
> Sel #23/B#23/C#23/D#23/E#23/F#23/G
Unknown command: Sel #23/B#23/C#23/D#23/E#23/F#23/G
> select #23/B#23/C#23/D#23/E#23/F#23/G
9312 atoms, 9396 bonds, 612 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel royal blue
> color sel dodger blue
> color sel royal blue
> select clear
> show #21 models
> select #21
3398 atoms, 3015 bonds, 823 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide #23 models
> delete atoms sel
> delete bonds sel
> open 4RS2 fromDatabase pdb format mmcif
4rs2 title:
1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
Escherichia coli in Complex with CoA [more info...]
Chain information for 4rs2 #21
---
Chain | Description | UniProt
A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167
Non-standard residues in 4rs2 #21
---
COA — coenzyme A
4rs2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
331 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #23 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
> matchmaker #23 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875
RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
0.339)
> show #1 models
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> matchmaker #21 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
(#21), sequence alignment score = 836
RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
0.670)
> select #21/A
1678 atoms, 1491 bonds, 404 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #21 models
> select #1
2107 atoms, 2148 bonds, 268 residues, 1 model selected
> show sel atoms
> select #1/C:1@CO
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
2106 atoms, 2148 bonds, 267 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/C:1@CO
1 atom, 1 residue, 1 model selected
> select ::name="CO"
15 atoms, 15 residues, 15 models selected
> ui tool show "Color Actions"
> color sel dim gray
> select clear
> show #21 models
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_0.cif
Chain information for fold_hqba_hfq1_65x6_co_model_0.cif #24
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_1.cif
Chain information for fold_hqba_hfq1_65x6_co_model_1.cif #25
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_2.cif
Chain information for fold_hqba_hfq1_65x6_co_model_2.cif #26
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_3.cif
Chain information for fold_hqba_hfq1_65x6_co_model_3.cif #27
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_4.cif
Chain information for fold_hqba_hfq1_65x6_co_model_4.cif #28
---
Chain | Description
A | .
B C D E F G | .
> hide #21 models
> select #24#25#26#27#28
22010 atoms, 22395 bonds, 2790 residues, 5 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
[Repeated 4 time(s)]
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_0.cif
Chain information for fold_hqba_hfqx6_co_model_0.cif #29
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_1.cif
Chain information for fold_hqba_hfqx6_co_model_1.cif #30
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_2.cif
Chain information for fold_hqba_hfqx6_co_model_2.cif #31
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_3.cif
Chain information for fold_hqba_hfqx6_co_model_3.cif #32
---
Chain | Description
A | .
B C D E F G | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_4.cif
Chain information for fold_hqba_hfqx6_co_model_4.cif #33
---
Chain | Description
A | .
B C D E F G | .
> select add #29
28038 atoms, 28536 bonds, 3570 residues, 6 models selected
> select add #30
34066 atoms, 34677 bonds, 4350 residues, 7 models selected
> select add #31
40094 atoms, 40818 bonds, 5130 residues, 8 models selected
> select add #32
46122 atoms, 46959 bonds, 5910 residues, 9 models selected
> select add #33
52150 atoms, 53100 bonds, 6690 residues, 10 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
[Repeated 4 time(s)]
> select #1
2107 atoms, 2148 bonds, 268 residues, 1 model selected
> select #1/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #24-33 to #1 & sel
Computing secondary structure
[Repeated 10 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_0.cif, chain A (#24), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.225 angstroms; (across all 167 pairs:
0.225)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_1.cif, chain A (#25), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.181 angstroms; (across all 167 pairs:
0.181)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_2.cif, chain A (#26), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.299 angstroms; (across all 167 pairs:
0.299)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_3.cif, chain A (#27), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.368 angstroms; (across all 167 pairs:
0.368)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfq1_65x6_co_model_4.cif, chain A (#28), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.255 angstroms; (across all 167 pairs:
0.255)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_0.cif, chain A (#29), sequence alignment score =
867.8
RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
0.202)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_1.cif, chain A (#30), sequence alignment score =
864.8
RMSD between 167 pruned atom pairs is 0.220 angstroms; (across all 167 pairs:
0.220)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_2.cif, chain A (#31), sequence alignment score =
864.8
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_3.cif, chain A (#32), sequence alignment score =
868.4
RMSD between 167 pruned atom pairs is 0.264 angstroms; (across all 167 pairs:
0.264)
Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
fold_hqba_hfqx6_co_model_4.cif, chain A (#33), sequence alignment score =
864.8
RMSD between 167 pruned atom pairs is 0.315 angstroms; (across all 167 pairs:
0.315)
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> hide #25 models
> hide #26 models
> hide #27 models
> hide #28 models
> hide #30 models
> hide #31 models
> show #31 models
> show #30 models
> show #25 models
> show #26 models
> show #27 models
> show #28 models
> hide #25 models
> hide #24 models
> hide #33 models
> hide #29 models
> show #25 models
> show #33 models
> select add #24
5713 atoms, 5820 bonds, 725 residues, 2 models selected
> select subtract #24
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select add #25
5713 atoms, 5820 bonds, 725 residues, 2 models selected
> select add #26
10115 atoms, 10299 bonds, 1283 residues, 3 models selected
> select add #27
14517 atoms, 14778 bonds, 1841 residues, 4 models selected
> select add #28
18919 atoms, 19257 bonds, 2399 residues, 5 models selected
> select add #30
24947 atoms, 25398 bonds, 3179 residues, 6 models selected
> select add #31
30975 atoms, 31539 bonds, 3959 residues, 7 models selected
> select add #32
37003 atoms, 37680 bonds, 4739 residues, 8 models selected
> select add #33
43031 atoms, 43821 bonds, 5519 residues, 9 models selected
> select add #1
43827 atoms, 44628 bonds, 5620 residues, 9 models selected
> hide #1 models
> select subtract #1
41720 atoms, 42480 bonds, 5352 residues, 8 models selected
> delete atoms sel
> delete bonds sel
> show #1 models
> show #21 models
> hide #21 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> select ::name="CO"
17 atoms, 17 residues, 17 models selected
> show sel & #1-5 atoms
> select #4/A:32
10 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> ui tool show "Color Actions"
> color sel magenta
> select clear
> select add #2
2107 atoms, 2148 bonds, 268 residues, 1 model selected
> select add #3
4214 atoms, 4296 bonds, 536 residues, 2 models selected
> select add #4
6321 atoms, 6444 bonds, 804 residues, 3 models selected
> select add #5
8428 atoms, 8592 bonds, 1072 residues, 4 models selected
> select clear
> show #21 models
> select #21/B:-10
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #21/B:0
21 atoms, 20 bonds, 2 residues, 1 model selected
> select add #21/B:-1
29 atoms, 27 bonds, 3 residues, 1 model selected
> select add #21/B:-2
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #21/B:-3
41 atoms, 38 bonds, 5 residues, 1 model selected
> select add #21/B:-4
49 atoms, 45 bonds, 6 residues, 1 model selected
> select add #21/B:-5
56 atoms, 51 bonds, 7 residues, 1 model selected
> select add #21/B:-6
66 atoms, 61 bonds, 8 residues, 1 model selected
> select add #21/B:-7
76 atoms, 71 bonds, 9 residues, 1 model selected
> select add #21/B:-8
86 atoms, 81 bonds, 10 residues, 1 model selected
> select add #21/B:-9
96 atoms, 91 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select clear
> select ::name="HIS"
3382 atoms, 3436 bonds, 313 residues, 24 models selected
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #21 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #4 models
> hide #2 models
> hide #3 models
> hide #5 models
> select #1/A:32
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel magenta
> hide sel atoms
> show sel atoms
> select clear
> show #21 models
> show #29 models
> hide #21 models
> hide #1 models
> show #23 models
> hide #29 models
> select #23/G:30
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #23/G:31
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> show #29 models
> hide #23 models
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #23 models
> hide #23 models
> show #1 models
> hide #1 models
> color sel cornflower blue
> select clear
> show #23 models
> hide #29 models
> show #29 models
> hide #23 models
> hide #29 models
> show #29 models
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> undo
[Repeated 9 time(s)]
> ui tool show "Color Actions"
> color sel pale violet red
> color sel light pink
> color sel hot pink
> color sel plum
> select clear
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel plum
> color sel violet
> select clear
> select #29/G:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #29/A:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #29/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
Drag select of 3 residues
> select clear
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #29/A:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium blue
> select clear
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> show #23 models
> select #23/C:31
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> hide #23 models
> select #29/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> color sel tan
> select clear
> select #29/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel royal blue
> select #29/G:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> show #21 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni.cxs
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_0.cif
Chain information for fold_azor_monomer_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_1.cif
Chain information for fold_azor_monomer_model_1.cif #2
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_2.cif
Chain information for fold_azor_monomer_model_2.cif #3
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_3.cif
Chain information for fold_azor_monomer_model_3.cif #4
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer/fold_azor_monomer_model_4.cif
Chain information for fold_azor_monomer_model_4.cif #5
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
---
note | Fetching CCD FAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/FAD/FAD.cif
Chain information for fold_azor_monomer_fad_model_0.cif #6
---
Chain | Description
A | .
Computing secondary structure
> rainbow
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_1.cif
Chain information for fold_azor_monomer_fad_model_1.cif #7
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_2.cif
Chain information for fold_azor_monomer_fad_model_2.cif #8
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_3.cif
Chain information for fold_azor_monomer_fad_model_3.cif #9
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_4.cif
Chain information for fold_azor_monomer_fad_model_4.cif #10
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif
Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif
---
note | Fetching CCD NAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/NAD/NAD.cif
Chain information for fold_azor_monomer_nad_model_0.cif #11
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_1.cif
Chain information for fold_azor_monomer_nad_model_1.cif #12
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_2.cif
Chain information for fold_azor_monomer_nad_model_2.cif #13
---
Chain | Description
A | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_3.cif
Chain information for fold_azor_monomer_nad_model_3.cif #14
---
Chain | Description
A | .
Computing secondary structure
[Repeated 1 time(s)]
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_4.cif
Chain information for fold_azor_monomer_nad_model_4.cif #15
---
Chain | Description
A | .
Computing secondary structure
> matchmaker #2-12 to #1
Computing secondary structure
[Repeated 11 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_1.cif, chain A (#2), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.117 angstroms; (across all 208 pairs:
0.117)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_2.cif, chain A (#3), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.103 angstroms; (across all 208 pairs:
0.103)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_3.cif, chain A (#4), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.129 angstroms; (across all 208 pairs:
0.129)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_4.cif, chain A (#5), sequence alignment score = 1086.8
RMSD between 208 pruned atom pairs is 0.121 angstroms; (across all 208 pairs:
0.121)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_1.cif, chain A (#7), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_2.cif, chain A (#8), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.447 angstroms; (across all 208 pairs:
0.447)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_3.cif, chain A (#9), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.420 angstroms; (across all 208 pairs:
0.420)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_4.cif, chain A (#10), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.291 angstroms; (across all 208 pairs:
0.291)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_1.cif, chain A (#12), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.353 angstroms; (across all 208 pairs:
0.353)
> matchmaker #13-15 to #1
Computing secondary structure
[Repeated 3 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_2.cif, chain A (#13), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.368 angstroms; (across all 208 pairs:
0.368)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_3.cif, chain A (#14), sequence alignment score =
1080.2
RMSD between 208 pruned atom pairs is 0.329 angstroms; (across all 208 pairs:
0.329)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_4.cif, chain A (#15), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.287 angstroms; (across all 208 pairs:
0.287)
> select add #2
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> select add #3
3292 atoms, 3370 bonds, 416 residues, 2 models selected
> select add #4
4938 atoms, 5055 bonds, 624 residues, 3 models selected
> select add #5
6584 atoms, 6740 bonds, 832 residues, 4 models selected
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> delete atoms sel
> delete bonds sel
> show #6 models
> hide #6 models
> show #6 models
> show #7 models
> hide #1 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> select add #7
1699 atoms, 1743 bonds, 209 residues, 1 model selected
> select add #8
3398 atoms, 3486 bonds, 418 residues, 2 models selected
> select add #9
5097 atoms, 5229 bonds, 627 residues, 3 models selected
> select add #10
6796 atoms, 6972 bonds, 836 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #11 models
> hide #6 models
> show #12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> show #13 models
> show #14 models
> show #15 models
> select add #12
1690 atoms, 1733 bonds, 209 residues, 1 model selected
> select add #13
3380 atoms, 3466 bonds, 418 residues, 2 models selected
> select add #14
5070 atoms, 5199 bonds, 627 residues, 3 models selected
> select add #15
6760 atoms, 6932 bonds, 836 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> show #1 models
> show #6 models
> hide #6 models
> hide #11 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_0.cif
Chain information for fold_azor_dimer_model_0.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_1.cif
Chain information for fold_azor_dimer_model_1.cif #3
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_2.cif
Chain information for fold_azor_dimer_model_2.cif #4
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_3.cif
Chain information for fold_azor_dimer_model_3.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_4.cif
Chain information for fold_azor_dimer_model_4.cif #7
---
Chain | Description
A B | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-7,11 to #1
Computing secondary structure
[Repeated 7 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_1.cif, chain A (#3), sequence alignment score = 1080.8
RMSD between 208 pruned atom pairs is 0.383 angstroms; (across all 208 pairs:
0.383)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_2.cif, chain A (#4), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.452 angstroms; (across all 208 pairs:
0.452)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_3.cif, chain A (#5), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.377 angstroms; (across all 208 pairs:
0.377)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_4.cif, chain A (#7), sequence alignment score = 1077.8
RMSD between 208 pruned atom pairs is 0.371 angstroms; (across all 208 pairs:
0.371)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
> show #6 models
> hide #2 models
> show #2 models
> hide #7 models
> hide #6 models
> show #7 models
> select add #3
3292 atoms, 3370 bonds, 416 residues, 1 model selected
> select add #4
6584 atoms, 6740 bonds, 832 residues, 2 models selected
> select add #5
9876 atoms, 10110 bonds, 1248 residues, 3 models selected
> select add #7
13168 atoms, 13480 bonds, 1664 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> hide #1 models
> show #6 models
> hide #2 models
> select /A
6584 atoms, 6740 bonds, 832 residues, 4 models selected
> show sel & #6 surfaces
> show #2 models
> select /B
1743 atoms, 1791 bonds, 210 residues, 3 models selected
> hide #2 models
> show #2 models
> select #2/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> hide #!6 models
> show #1 models
> show #!6 models
> hide #1 models
> hide #!6 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_0.cif
Chain information for fold_azor_dimer_fad_model_0.cif #3
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_1.cif
Chain information for fold_azor_dimer_fad_model_1.cif #4
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_2.cif
Chain information for fold_azor_dimer_fad_model_2.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> hide sel surfaces
> ui tool show Matchmaker
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_3.cif
Chain information for fold_azor_dimer_fad_model_3.cif #7
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_4.cif
Chain information for fold_azor_dimer_fad_model_4.cif #8
---
Chain | Description
A B | .
Computing secondary structure
[Repeated 1 time(s)]
> matchmaker #3-5,7-8#!6 to #1
Computing secondary structure
[Repeated 6 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_1.cif, chain A (#4), sequence alignment score = 1049
RMSD between 208 pruned atom pairs is 0.456 angstroms; (across all 208 pairs:
0.456)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_2.cif, chain A (#5), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.435 angstroms; (across all 208 pairs:
0.435)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_3.cif, chain A (#7), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.408 angstroms; (across all 208 pairs:
0.408)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_4.cif, chain A (#8), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.428 angstroms; (across all 208 pairs:
0.428)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
——— End of log from Wed Feb 18 08:19:31 2026 ———
opened ChimeraX session
> hide #!2 models
> hide #4 models
> hide #5 models
> hide #7 models
> hide #8 models
> show #4 models
> hide #3 models
> show #5 models
> show #7 models
> show #8 models
> select add #4
4991 atoms, 5113 bonds, 625 residues, 2 models selected
> select add #5
8336 atoms, 8541 bonds, 1042 residues, 3 models selected
> select add #7
11681 atoms, 11969 bonds, 1459 residues, 4 models selected
> select add #8
15026 atoms, 15397 bonds, 1876 residues, 5 models selected
> delete atoms (#4-5,7-8 & sel)
> delete bonds (#4-5,7-8 & sel)
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
Chain information for fold_azor_monomer_fad_model_0.cif #4
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_nad/fold_azor_dimer_nad_model_0.cif
Chain information for fold_azor_dimer_nad_model_0.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/icd/fold_icd_model_0.cif
Chain information for fold_icd_model_0.cif #7
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/mqo/fold_mqo_model_0.cif
Chain information for fold_mqo_model_0.cif #8
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/ndhc/fold_ndhc_model_0.cif
Chain information for fold_ndhc_model_0.cif #9
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/ndhf/fold_ndhf_model_0.cif
Chain information for fold_ndhf_model_0.cif #10
---
Chain | Description
A | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/suca/fold_suca_model_0.cif
Chain information for fold_suca_model_0.cif #12
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #3-5,7-12#!2,6 to #1/A pairing bs
Computing secondary structure
[Repeated 6 time(s)] Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain B (#5), sequence alignment score =
1086.8
RMSD between 208 pruned atom pairs is 0.362 angstroms; (across all 208 pairs:
0.362)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
> hide #12 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> show #1 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> hide #5 models
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #4 models
> show #3 models
> hide #!2 models
> hide #1 models
> show #!6 models
> hide #3#!6 surfaces
> show #7 models
> hide #!6 models
> hide #3 models
> show #8 models
> hide #7 models
> show #9 models
> hide #8 models
> rainbow #9
> show #10 models
> hide #9 models
> show #11 models
> hide #10 models
> show #1 models
> hide #1 models
> show #1 models
> hide #11 models
> show #11 models
> show #12 models
> hide #11 models
> hide #1 models
> matchmaker #8-10,12 to #7/A pairing bs
Computing secondary structure
[Repeated 4 time(s)] Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_suca_model_0.cif,
chain A (#12), sequence alignment score = 124
RMSD between 16 pruned atom pairs is 1.040 angstroms; (across all 346 pairs:
29.841)
> show #7 models
> hide #12 models
> show #8 models
> show #9 models
> hide #8 models
> hide #7 models
> show #8 models
> hide #9 models
> show #12 models
> hide #8 models
> rainbow #12
> show #7 models
> hide #12 models
> show #8 models
> hide #7 models
> show #5 models
> hide #8 models
> color #5 bychain
> show #!6 models
> hide #5 models
> show #11 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #5 models
> select /A
32114 atoms, 32801 bonds, 4077 residues, 12 models selected
> ui tool show Matchmaker
> matchmaker #3-5,7-12#!2,6 & sel to #1/A & sel pairing bs
Computing secondary structure
[Repeated 6 time(s)] Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.359 angstroms; (across all 208 pairs:
0.359)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)
> show #1 models
> hide #1 models
> show #5 models
> hide #11 models
> show #11 models
> hide #5 models
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> select ~sel & ##selected
4938 atoms, 5055 bonds, 624 residues, 2 models selected
> rainbow sel & #11
> select clear
> show #1 models
> hide #11 models
> open 9H2I fromDatabase pdb format mmcif
Summary of feedback from opening 9H2I fetched from pdb
---
note | Fetching compressed mmCIF 9h2i from http://files.rcsb.org/download/9h2i.cif
9h2i title:
Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of
Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate
dehydrogenase complex [more info...]
Chain information for 9h2i #13
---
Chain | Description | UniProt
A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex | ODP2_ECOLI 314-379
B C | Dihydrolipoyl dehydrogenase | DLDH_ECOLI 2-474
Non-standard residues in 9h2i #13
---
FAD — flavin-adenine dinucleotide
> ui tool show Matchmaker
> matchmaker #13 to #1/A pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with 9h2i, chain B
(#13), sequence alignment score = 64.3
RMSD between 6 pruned atom pairs is 0.906 angstroms; (across all 61 pairs:
18.939)
> undo
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> hide #11 models
> hide #1 models
> show #4 models
> hide #13 models
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> show #13 models
> hide #4 models
> color sel & #13 bychain
> undo
> select clear
> color #13 bychain
> undo
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> matchmaker #13 & sel to #4/A & sel pairing bs
No 'to' chains specified
> matchmaker #13 & sel to #4/A & sel pairing bs
No 'to' chains specified
> matchmaker #13 & sel to #6 & sel
No matrix compatible with both reference structure and all match structures
> select clear
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> matchmaker #13 to #6 & sel
No matrix compatible with both reference structure and all match structures
> matchmaker #13 to #6
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_fad_model_0.cif, chain A (#6) with 9h2i, chain B
(#13), sequence alignment score = 64.3
RMSD between 6 pruned atom pairs is 0.976 angstroms; (across all 61 pairs:
18.887)
> show #!6 models
> hide #13 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open 8RX4 fromDatabase pdb format mmcif
Summary of feedback from opening 8RX4 fetched from pdb
---
notes | Fetching compressed mmCIF 8rx4 from http://files.rcsb.org/download/8rx4.cif
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
8rx4 title:
Mycothione reductase from Mycobacterium xenopi in complex with co-factor FAD
and redox co-factor NADP(H) [more info...]
Chain information for 8rx4 #14
---
Chain | Description | UniProt
A B | Mycothione reductase | X8E6Y0_MYCXE 1-459
Non-standard residues in 8rx4 #14
---
FAD — flavin-adenine dinucleotide
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)
> hide #!6 models
> matchmaker #14 to #13
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)
> show #13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> color sel & #13-14 bychain
> select clear
> hide #14 models
> show #14 models
> hide #13 models
> show #13 models
> hide #14 models
> show #14 models
> hide #13 models
> select #14/B
3646 atoms, 3705 bonds, 481 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #13 models
> hide #14 models
> select #13/C
3803 atoms, 3650 bonds, 693 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> select #13/B
3924 atoms, 3668 bonds, 798 residues, 1 model selected
> rainbow sel
> select clear
> show #4 models
> hide #13 models
> show #14 models
> show #13 models
> hide #14 models
> hide #4 models
> show #!6 models
> hide #13 models
> show #13 models
> select #13/B:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/B:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "move picked models"
> view matrix models
> #13,-0.24553,0.95614,-0.15973,-12.311,-0.87052,-0.14498,0.4703,-33.244,0.42651,0.25452,0.86793,37.123
> select clear
> show #3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> hide #13 models
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> color sel & #3 bychain
> select clear
> show #13 models
> select #13/B:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.033187,-0.97762,-0.20777,14.167,0.99779,0.020425,0.063272,41.991,-0.057612,-0.20941,0.97613,20.908
> view matrix models
> #13,0.61108,-0.5049,-0.60964,43.097,0.74854,0.11812,0.65248,13.491,-0.25743,-0.85506,0.45012,36.524
Drag select of 1 residues
> view matrix models
> #13,0.69637,-0.51088,-0.50406,42.577,0.69997,0.32838,0.6342,10.762,-0.15848,-0.79446,0.58627,34.933
> view matrix models
> #13,0.60362,-0.77451,-0.18916,31.241,0.57555,0.25913,0.77562,2.4774,-0.55171,-0.57705,0.60219,19.363
> view matrix models
> #13,0.57452,-0.7742,-0.2656,32.755,0.56401,0.13931,0.81393,1.7918,-0.59314,-0.61742,0.5167,21.081
> view matrix models
> #13,0.50768,-0.80838,-0.29797,31.826,0.63814,0.12046,0.76044,6.2021,-0.57883,-0.57621,0.57701,19.262
> view matrix models
> #13,0.41134,-0.8476,-0.33522,30.098,0.72496,0.081317,0.68397,11.956,-0.55248,-0.52437,0.64793,17.418
> view matrix models
> #13,0.50347,-0.56782,-0.65123,41.319,0.83944,0.14298,0.52431,20.563,-0.2046,-0.81064,0.54863,34.733
> view matrix models
> #13,0.81357,-0.39993,-0.42208,42.973,0.56489,0.37157,0.73677,2.4881,-0.13783,-0.83785,0.52822,37.879
> select clear
> select #13/B:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #13,0.81385,-0.37394,-0.44476,43.517,0.57225,0.38291,0.7252,3.0254,-0.10088,-0.84472,0.52562,39.27
> view matrix models
> #13,0.80931,-0.3118,-0.49779,44.601,0.58724,0.41087,0.69738,4.2194,-0.01291,-0.85672,0.51563,42.67
> view matrix models
> #13,0.83554,-0.52523,-0.16124,36.183,0.53716,0.84258,0.038938,20.618,0.11541,-0.11915,0.98615,25.714
> view matrix models
> #13,0.85682,-0.51537,0.016019,31.023,0.50956,0.85108,0.12652,16.749,-0.07884,-0.10025,0.99183,18.802
> view matrix models
> #13,0.13465,-0.7299,-0.67016,30.752,0.80312,-0.31576,0.50527,23.627,-0.58041,-0.60625,0.54368,20.54
> select clear
[Repeated 1 time(s)]Drag select of 5 residues, 1 bonds
> show #5 models
> hide #3 models
> show #3 models
> hide #5 models
> show #14 models
> matchmaker #14 to #13
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)
> hide #13 models
> show #13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> show sel & #3,13-14 surfaces
> hide #!14 models
> hide sel & #!3,13 surfaces
> show #!14 models
> hide #!13 models
> hide sel & #!3,14 surfaces
> select clear
> hide #!3 models
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> select ::name="NAP"
96 atoms, 104 bonds, 2 residues, 1 model selected
> show #!13 models
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> rainbow sel & #!14
> select clear
> select ::name="NAP"
96 atoms, 104 bonds, 2 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 217
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.051654 seconds
| QMMM: Dspev diag routine = 0.044332 seconds
| QMMM: Dspevd diag routine = 0.032116 seconds
| QMMM: Dspevx diag routine = 0.153242 seconds
| QMMM: Dsyev diag routine = 0.047097 seconds
| QMMM: Dsyevd diag routine = 0.033935 seconds
| QMMM: Dsyevr diag routine = 0.038554 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.022789 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 P 17.4620 0.4650 57.8060
QMMM: 2 2 O 16.5620 -0.5740 58.3900
QMMM: 3 3 O 18.0440 0.2210 56.4520
QMMM: 4 4 O 18.6480 0.7880 58.8450
QMMM: 5 5 C 18.2700 1.3930 60.1070
QMMM: 6 6 C 19.4870 1.8540 60.8730
QMMM: 7 7 O 19.0230 2.6210 62.0160
QMMM: 8 8 C 20.3910 0.7570 61.4600
QMMM: 9 9 O 21.7470 1.1830 61.4090
QMMM: 10 10 C 19.8810 0.6600 62.8920
QMMM: 11 11 O 20.8230 0.1440 63.8270
QMMM: 12 12 C 19.6340 2.1310 63.1840
QMMM: 13 13 N 18.7140 2.3450 64.2950
QMMM: 14 14 C 17.4200 1.8950 64.3780
QMMM: 15 15 N 16.8230 2.2310 65.4940
QMMM: 16 16 C 17.7860 2.9360 66.2020
QMMM: 17 17 C 17.7680 3.5530 67.4670
QMMM: 18 18 N 16.7090 3.5600 68.2720
QMMM: 19 19 N 18.9020 4.1690 67.8780
QMMM: 20 20 C 19.9640 4.1590 67.0630
QMMM: 21 21 N 20.0960 3.6140 65.8570
QMMM: 22 22 C 18.9590 3.0090 65.4750
QMMM: 23 23 O 16.6940 1.8750 57.8220
QMMM: 24 24 P 16.8310 3.1760 56.8950
QMMM: 25 25 O 16.1610 4.3450 57.5500
QMMM: 26 26 O 18.2590 3.2930 56.4770
QMMM: 27 27 O 15.9430 2.7150 55.6410
QMMM: 28 28 C 14.5280 2.4980 55.8770
QMMM: 29 29 C 13.9670 1.5170 54.8750
QMMM: 30 30 O 14.0230 2.0920 53.5500
QMMM: 31 31 C 14.6700 0.1520 54.7880
QMMM: 32 32 O 13.7350 -0.9120 54.6620
QMMM: 33 33 C 15.5640 0.2940 53.5490
QMMM: 34 34 O 15.7840 -0.9330 52.8700
QMMM: 35 35 C 14.7120 1.2110 52.6690
QMMM: 36 36 N 15.5520 2.0170 51.7640
QMMM: 37 37 C 15.9700 1.4830 50.5670
QMMM: 38 38 C 16.8040 2.2160 49.7300
QMMM: 39 39 C 17.2170 1.5960 48.4310
QMMM: 40 40 O 16.7920 0.4660 48.1440
QMMM: 41 41 N 18.0490 2.2680 47.6420
QMMM: 42 42 C 17.1960 3.4950 50.0970
QMMM: 43 43 C 16.7690 4.0240 51.3000
QMMM: 44 44 C 15.9580 3.2770 52.1340
QMMM: 45 45 P 20.6860 -1.4490 64.0240
QMMM: 46 46 O 21.7060 -1.8020 65.0890
QMMM: 47 47 O 21.0090 -2.0990 62.6800
QMMM: 48 48 O 19.2630 -1.7280 64.4740
QMMM: 49 49 H 17.7290 0.6600 60.7060
QMMM: 50 50 H 17.6220 2.2480 59.9150
QMMM: 51 51 H 20.0850 2.5010 60.2310
QMMM: 52 52 H 20.2560 -0.1860 60.9310
QMMM: 53 53 H 22.3250 0.4250 61.5240
QMMM: 54 54 H 18.9490 0.0970 62.9320
QMMM: 55 55 H 20.5770 2.6470 63.3660
QMMM: 56 56 H 16.9410 1.3200 63.5990
QMMM: 57 57 H 15.8540 3.1050 67.9850
QMMM: 58 58 H 16.7600 4.0200 69.1700
QMMM: 59 59 H 20.8400 4.6670 67.4390
QMMM: 60 60 H 14.0000 3.4470 55.7840
QMMM: 61 61 H 14.3870 2.1050 56.8840
QMMM: 62 62 H 12.9200 1.3420 55.1230
QMMM: 63 63 H 15.2870 -0.0020 55.6730
QMMM: 64 64 H 13.8800 -1.5500 55.3640
QMMM: 65 65 H 16.5100 0.7710 53.8050
QMMM: 66 66 H 16.3180 -1.5120 53.4190
QMMM: 67 67 H 13.9980 0.6220 52.0930
QMMM: 68 68 H 15.6500 0.4930 50.2770
QMMM: 69 69 H 18.3800 3.1810 47.9180
QMMM: 70 70 H 18.3500 1.8650 46.7660
QMMM: 71 71 H 17.8320 4.0750 49.4450
QMMM: 72 72 H 17.0690 5.0210 51.5890
QMMM: 73 73 H 15.6420 3.6860 53.0820
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2168E+07 DeltaE = -0.4757E+03 DeltaP = 0.9525E+00
QMMM: Smallest DeltaE = 0.8289E-07 DeltaP = 0.1057E-04 Step = 3
Failure running ANTECHAMBER for residue NAP Check reply log for details
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 217
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.050281 seconds
| QMMM: Dspev diag routine = 0.043968 seconds
| QMMM: Dspevd diag routine = 0.032120 seconds
| QMMM: Dspevx diag routine = 0.153124 seconds
| QMMM: Dsyev diag routine = 0.047103 seconds
| QMMM: Dsyevd diag routine = 0.033926 seconds
| QMMM: Dsyevr diag routine = 0.039887 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.024004 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 P 17.4620 0.4650 57.8060
QMMM: 2 2 O 16.5620 -0.5740 58.3900
QMMM: 3 3 O 18.0440 0.2210 56.4520
QMMM: 4 4 O 18.6480 0.7880 58.8450
QMMM: 5 5 C 18.2700 1.3930 60.1070
QMMM: 6 6 C 19.4870 1.8540 60.8730
QMMM: 7 7 O 19.0230 2.6210 62.0160
QMMM: 8 8 C 20.3910 0.7570 61.4600
QMMM: 9 9 O 21.7470 1.1830 61.4090
QMMM: 10 10 C 19.8810 0.6600 62.8920
QMMM: 11 11 O 20.8230 0.1440 63.8270
QMMM: 12 12 C 19.6340 2.1310 63.1840
QMMM: 13 13 N 18.7140 2.3450 64.2950
QMMM: 14 14 C 17.4200 1.8950 64.3780
QMMM: 15 15 N 16.8230 2.2310 65.4940
QMMM: 16 16 C 17.7860 2.9360 66.2020
QMMM: 17 17 C 17.7680 3.5530 67.4670
QMMM: 18 18 N 16.7090 3.5600 68.2720
QMMM: 19 19 N 18.9020 4.1690 67.8780
QMMM: 20 20 C 19.9640 4.1590 67.0630
QMMM: 21 21 N 20.0960 3.6140 65.8570
QMMM: 22 22 C 18.9590 3.0090 65.4750
QMMM: 23 23 O 16.6940 1.8750 57.8220
QMMM: 24 24 P 16.8310 3.1760 56.8950
QMMM: 25 25 O 16.1610 4.3450 57.5500
QMMM: 26 26 O 18.2590 3.2930 56.4770
QMMM: 27 27 O 15.9430 2.7150 55.6410
QMMM: 28 28 C 14.5280 2.4980 55.8770
QMMM: 29 29 C 13.9670 1.5170 54.8750
QMMM: 30 30 O 14.0230 2.0920 53.5500
QMMM: 31 31 C 14.6700 0.1520 54.7880
QMMM: 32 32 O 13.7350 -0.9120 54.6620
QMMM: 33 33 C 15.5640 0.2940 53.5490
QMMM: 34 34 O 15.7840 -0.9330 52.8700
QMMM: 35 35 C 14.7120 1.2110 52.6690
QMMM: 36 36 N 15.5520 2.0170 51.7640
QMMM: 37 37 C 15.9700 1.4830 50.5670
QMMM: 38 38 C 16.8040 2.2160 49.7300
QMMM: 39 39 C 17.2170 1.5960 48.4310
QMMM: 40 40 O 16.7920 0.4660 48.1440
QMMM: 41 41 N 18.0490 2.2680 47.6420
QMMM: 42 42 C 17.1960 3.4950 50.0970
QMMM: 43 43 C 16.7690 4.0240 51.3000
QMMM: 44 44 C 15.9580 3.2770 52.1340
QMMM: 45 45 P 20.6860 -1.4490 64.0240
QMMM: 46 46 O 21.7060 -1.8020 65.0890
QMMM: 47 47 O 21.0090 -2.0990 62.6800
QMMM: 48 48 O 19.2630 -1.7280 64.4740
QMMM: 49 49 H 17.7290 0.6600 60.7060
QMMM: 50 50 H 17.6220 2.2480 59.9150
QMMM: 51 51 H 20.0850 2.5010 60.2310
QMMM: 52 52 H 20.2560 -0.1860 60.9310
QMMM: 53 53 H 22.3250 0.4250 61.5240
QMMM: 54 54 H 18.9490 0.0970 62.9320
QMMM: 55 55 H 20.5770 2.6470 63.3660
QMMM: 56 56 H 16.9410 1.3200 63.5990
QMMM: 57 57 H 15.8540 3.1050 67.9850
QMMM: 58 58 H 16.7600 4.0200 69.1700
QMMM: 59 59 H 20.8400 4.6670 67.4390
QMMM: 60 60 H 14.0000 3.4470 55.7840
QMMM: 61 61 H 14.3870 2.1050 56.8840
QMMM: 62 62 H 12.9200 1.3420 55.1230
QMMM: 63 63 H 15.2870 -0.0020 55.6730
QMMM: 64 64 H 13.8800 -1.5500 55.3640
QMMM: 65 65 H 16.5100 0.7710 53.8050
QMMM: 66 66 H 16.3180 -1.5120 53.4190
QMMM: 67 67 H 13.9980 0.6220 52.0930
QMMM: 68 68 H 15.6500 0.4930 50.2770
QMMM: 69 69 H 18.3800 3.1810 47.9180
QMMM: 70 70 H 18.3500 1.8650 46.7660
QMMM: 71 71 H 17.8320 4.0750 49.4450
QMMM: 72 72 H 17.0690 5.0210 51.5890
QMMM: 73 73 H 15.6420 3.6860 53.0820
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2168E+07 DeltaE = -0.4757E+03 DeltaP = 0.9525E+00
QMMM: Smallest DeltaE = 0.8289E-07 DeltaP = 0.1057E-04 Step = 3
Failure running ANTECHAMBER for residue NAP Check reply log for details
> color bfactor sel
96 atoms, 2 residues, atom bfactor range 41.3 to 73.2
> select clear
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!6 models
> select #14/A:97
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.90725,0.31566,-0.27796,2.8054,0.29785,-0.01556,0.95449,-50.578,0.29696,-0.94875,-0.10814,46.454
> view matrix models
> #14,0.93295,0.28926,-0.21434,-0.73384,0.25781,-0.12123,0.95856,-50.42,0.25129,-0.94954,-0.18768,51.003
> view matrix models
> #14,0.95399,0.10503,0.28085,-26.454,-0.27841,-0.037495,0.95973,-44.999,0.11133,-0.99376,-0.0065275,43.104
> view matrix models
> #14,0.98633,-0.1547,0.056722,-15.368,-0.093531,-0.24224,0.9657,-47.262,-0.13566,-0.9578,-0.2534,58.309
> hide #!6 models
> show #4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #4 models
> show #5 models
> hide #!6 models
> show #!6 models
> hide #5 models
> select #14/A:60
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.98633,-0.1547,0.056722,5.0516,-0.093531,-0.24224,0.9657,-51.288,-0.13566,-0.9578,-0.2534,64.425
> view matrix models
> #14,0.98633,-0.1547,0.056722,10.913,-0.093531,-0.24224,0.9657,-51.526,-0.13566,-0.9578,-0.2534,63.602
> view matrix models
> #14,0.98633,-0.1547,0.056722,15.905,-0.093531,-0.24224,0.9657,-50.924,-0.13566,-0.9578,-0.2534,60.642
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.97926,-0.18136,0.090283,14.242,-0.086033,0.031182,0.9958,-52.444,-0.18342,-0.98292,0.014932,47.335
> select clear
> select #14/A:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #14,0.90266,-0.17746,0.39205,-0.47885,-0.41831,-0.14782,0.8962,-44.018,-0.10109,-0.97296,-0.20766,57.936
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.90266,-0.17746,0.39205,-2.5843,-0.41831,-0.14782,0.8962,-43.691,-0.10109,-0.97296,-0.20766,52.913
> select clear
> hide #!6 models
> show #!6 models
> select clear
Drag select of 26 atoms, 132 residues, 25 bonds
Drag select of 40 atoms, 192 residues, 36 bonds
> hide sel cartoons
> view matrix models
> #14,0.90266,-0.17746,0.39205,-4.6463,-0.41831,-0.14782,0.8962,-41.429,-0.10109,-0.97296,-0.20766,56.964
> select clear
[Repeated 1 time(s)]
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> select #14/A
3671 atoms, 3705 bonds, 506 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!3 models
> open 3w78 fromDatabase pdb format mmcif
Summary of feedback from opening 3w78 fetched from pdb
---
notes | Fetching compressed mmCIF 3w78 from http://files.rcsb.org/download/3w78.cif
Fetching CCD CBD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CBD/CBD.cif
Fetching CCD FMN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/FMN/FMN.cif
3w78 title:
Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor
Cibacron Blue [more info...]
Chain information for 3w78 #15
---
Chain | Description | UniProt
A B C D | FMN-dependent NADH-azoreductase | C0STY1_9BACI 1-211
Non-standard residues in 3w78 #15
---
CBD — cibacron blue
FMN — flavin mononucleotide (riboflavin monophosphate)
3w78 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> matchmaker #15 to #6
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_fad_model_0.cif, chain A (#6) with 3w78, chain A
(#15), sequence alignment score = 709.3
RMSD between 188 pruned atom pairs is 0.720 angstroms; (across all 207 pairs:
1.539)
> hide #!6 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> select #15/C
1697 atoms, 1735 bonds, 217 residues, 1 model selected
> select #15/C
1697 atoms, 1735 bonds, 217 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #15/D
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!3 models
> hide #!14 models
> hide #!3 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> rainbow sel
> select clear
> select #15/B
1696 atoms, 1735 bonds, 216 residues, 1 model selected
> rainbow sel
> select clear
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> select #3/B:169
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select clear
> show #15 models
> hide #15 models
> show #15 models
> select #3/B:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> select clear
> select #3/A:184
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #15 models
> select clear
> show #15 models
> select #15/B:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #15/A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #4 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select clear
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> select #15/B
1696 atoms, 1735 bonds, 216 residues, 1 model selected
> color sel light gray
> color sel gray
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #15/B:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/A:147
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> hide sel atoms
> select clear
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> select #3/B:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select clear
> select #3/B:124
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #3/B:126
5 atoms, 4 bonds, 1 residue, 1 model selected
> open 4m0C fromDatabase pdb format mmcif
Summary of feedback from opening 4m0C fetched from pdb
---
note | Fetching compressed mmCIF 4m0c from http://files.rcsb.org/download/4m0c.cif
4m0c title:
The crystal structure of a FMN-dependent NADH-azoreductase from Bacillus
anthracis str. Ames Ancestor in complex with FMN. [more info...]
Chain information for 4m0c #16
---
Chain | Description | UniProt
A B | FMN-dependent NADH-azoreductase 1 | AZOR1_BACAN 1-220
Non-standard residues in 4m0c #16
---
FMN — flavin mononucleotide (riboflavin monophosphate)
GOL — glycerol (glycerin; propane-1,2,3-triol)
ZN — zinc ion
> hide #15 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!3 models
> hide #!16 models
> show #15 models
> hide #15 models
> matchmaker #!16 to #3
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)
> show #!16 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> select #3/A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #3/A:28
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> show #!16 models
> select #3/A:24@NZ
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) blue
> select clear
> hide #!3 models
> show #!3 models
> select #3/B:60
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> color #!16 bypolymer
> color #!16 bychain
> undo
> show #!14 models
> hide #!14 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.699,0.94367,-0.25032,-0.21638,-0.059448,0.29722,0.92867,0.22188,0.19931
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.468,0.94367,-0.25032,-0.21638,0.097978,0.29722,0.92867,0.22188,1.1612
> show #!3 models
> hide #!3 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.206,0.94367,-0.25032,-0.21638,1.5618,0.29722,0.92867,0.22188,1.9041
> show #!3 models
> hide #!3 models
> show #15 models
> hide #!16 models
> hide #15 models
> show #15 models
> show #!16 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!16 models
> show #!3 models
> hide #15 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,3.1194,0.94367,-0.25032,-0.21638,-4.132,0.29722,0.92867,0.22188,5.8471
> select #/B
Expected an objects specifier or a keyword
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select #3/A:85
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #5 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #5 models
> hide #!3 models
> hide #!6 models
> show #8 models
> rainbow #8
> show #9 models
> hide #9 models
> show #9 models
> hide #8 models
> show #10 models
> hide #9 models
> rainbow #10
> show #9 models
> show #11 models
> hide #11 models
> ui tool show Matchmaker
> matchmaker #8-10 to #7
Computing secondary structure
[Repeated 3 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)
> view matrix models
> #3,0.14541,-0.27369,0.95076,8.5292,0.94367,-0.25032,-0.21638,-19.372,0.29722,0.92867,0.22188,0.15815
> hide #9 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> hide #12 models
> show #7 models
> rainbow #7
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> select #7/A:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.056929,0.94842,-0.31187,29.698,-0.99216,0.018927,-0.12355,27.519,-0.11127,0.31646,0.94206,-48.931
> ui mousemode right "rotate selected models"
> select #7/A:168
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.6578,0.45453,-0.60058,25.727,0.50261,-0.85878,-0.099448,19.133,-0.56096,-0.23644,-0.79336,-49.882
> view matrix models
> #7,0.60118,0.48068,-0.63838,25.96,0.54786,-0.82948,-0.10864,18.796,-0.58175,-0.28444,-0.76201,-49.624
> view matrix models
> #7,0.49131,0.84301,-0.21895,27.321,0.79014,-0.53716,-0.29517,16.511,-0.36645,-0.027978,-0.93002,-51.657
> view matrix models
> #7,0.29276,0.89319,-0.34133,28.206,0.88387,-0.38897,-0.25975,15.859,-0.36478,-0.22565,-0.90334,-51.396
> view matrix models
> #7,0.39394,0.66509,-0.6344,27.076,0.74669,-0.63405,-0.20106,17.118,-0.53597,-0.3945,-0.7464,-49.757
> view matrix models
> #7,0.3975,0.64273,-0.6549,27.026,0.73208,-0.65243,-0.19596,17.242,-0.55323,-0.40155,-0.72986,-49.601
> view matrix models
> #7,0.31312,0.65044,-0.69202,27.453,0.7722,-0.59855,-0.21318,16.892,-0.55286,-0.46763,-0.68969,-49.434
> view matrix models
> #7,0.41324,0.50876,-0.75524,26.815,0.7267,-0.68404,-0.06317,17.64,-0.54875,-0.52273,-0.6524,-49.31
> select clear
> hide #7 models
> show #8 models
> select #8/A:495
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.29707,0.95019,0.094245,27.561,-0.9516,-0.28647,-0.11132,28.24,-0.078773,-0.12275,0.98931,-51.568
> ui mousemode right "rotate selected models"
> select #8/A:464
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #8,-0.83282,-0.06747,-0.54942,33.938,0.53295,-0.36591,-0.76293,29.175,-0.14956,-0.9282,0.3407,-46.42
> view matrix models
> #8,-0.79413,0.58208,0.17476,27.984,0.60087,0.79512,0.08207,22.702,-0.09118,0.17018,-0.98119,-32.86
> view matrix models
> #8,-0.74237,-0.25474,0.61968,22.54,0.1102,0.86588,0.48796,20.688,-0.66087,0.43053,-0.61473,-33.983
> view matrix models
> #8,-0.85203,0.52313,0.019577,29.536,0.49615,0.81887,-0.28859,26.523,-0.167,-0.23617,-0.95725,-33.383
> view matrix models
> #8,-0.82201,-0.085732,0.56298,23.565,0.39872,0.61921,0.67646,17.631,-0.4066,0.78053,-0.47481,-35.657
> view matrix models
> #8,-0.96452,-0.0076278,0.26388,26.924,0.094374,0.92356,0.37165,21.898,-0.24655,0.38337,-0.89008,-32.89
> view matrix models
> #8,-0.97869,-0.027577,0.20348,27.504,0.057976,0.91351,0.40267,21.719,-0.19698,0.40588,-0.89245,-33.004
> view matrix models
> #8,-0.96042,0.18076,0.21192,27.65,0.26575,0.82255,0.50278,19.967,-0.083434,0.5392,-0.83803,-33.708
> view matrix models
> #8,-0.94381,0.13924,0.29972,26.723,0.29173,0.77716,0.5576,19.31,-0.15529,0.61371,-0.77411,-33.957
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> hide #8 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!16 models
> open 1v4B fromDatabase pdb format mmcif
Summary of feedback from opening 1v4B fetched from pdb
---
notes | Fetching compressed mmCIF 1v4b from http://files.rcsb.org/download/1v4b.cif
Fetching CCD IPA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif
1v4b title:
The crystal structure of AzoR (Azo Reductase) from Escherichia coli: Oxidized
form [more info...]
Chain information for 1v4b #17
---
Chain | Description | UniProt
A | NADH-azoreductase, FMN-dependent | ACPD_ECOLI 1-200
Non-standard residues in 1v4b #17
---
EDO — 1,2-ethanediol (ethylene glycol)
FMN — flavin mononucleotide (riboflavin monophosphate)
IPA — isopropyl alcohol (2-propanol)
1v4b mmCIF Assemblies
---
1| author_defined_assembly
> open 2B3D fromDatabase pdb format mmcif
Summary of feedback from opening 2B3D fetched from pdb
---
note | Fetching compressed mmCIF 2b3d from http://files.rcsb.org/download/2b3d.cif
2b3d title:
Crystal structure of Modulator of Drug activity B in complex with flavin
adenine dinucleotide [more info...]
Chain information for 2b3d #18
---
Chain | Description | UniProt
A B | Modulator of drug activity B | MDAB_ECOLI 13-204
Non-standard residues in 2b3d #18
---
FAD — flavin-adenine dinucleotide
> hide #!16 models
> hide #!17 models
> matchmaker #!18 to #3
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain B
(#18), sequence alignment score = 156.9
RMSD between 82 pruned atom pairs is 1.158 angstroms; (across all 168 pairs:
6.190)
> show #!3 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!6 models
> select /A
43169 atoms, 43600 bonds, 3 pseudobonds, 5896 residues, 20 models selected
> hide #!3 models
> show #!3 models
> show #7 models
> hide #7 models
> hide #!6 models
> matchmaker #1,4-5,7-12,15#!2,6,13-14,16-18 & sel to #3 & sel
Computing secondary structure
[Repeated 12 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.436 angstroms; (across all 208 pairs:
0.436)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1085
RMSD between 208 pruned atom pairs is 0.263 angstroms; (across all 208 pairs:
0.263)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1074.2
RMSD between 208 pruned atom pairs is 0.269 angstroms; (across all 208 pairs:
0.269)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 83.4
RMSD between 10 pruned atom pairs is 1.453 angstroms; (across all 169 pairs:
23.782)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 59.8
RMSD between 7 pruned atom pairs is 1.684 angstroms; (across all 65 pairs:
22.736)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 65.4
RMSD between 24 pruned atom pairs is 1.163 angstroms; (across all 154 pairs:
32.226)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 59.3
RMSD between 31 pruned atom pairs is 1.111 angstroms; (across all 142 pairs:
21.293)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 6 pruned atom pairs is 1.325 angstroms; (across all 101 pairs:
17.171)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 9h2i, chain A
(#13), sequence alignment score = 24
RMSD between 11 pruned atom pairs is 0.322 angstroms; (across all 26 pairs:
11.957)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 8rx4, chain A
(#14), sequence alignment score = 51.5
RMSD between 10 pruned atom pairs is 1.029 angstroms; (across all 173 pairs:
29.959)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 3w78, chain A
(#15), sequence alignment score = 716.5
RMSD between 189 pruned atom pairs is 0.774 angstroms; (across all 207 pairs:
1.461)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 1v4b, chain A
(#17), sequence alignment score = 427.4
RMSD between 135 pruned atom pairs is 1.176 angstroms; (across all 194 pairs:
2.701)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain A
(#18), sequence alignment score = 150.4
RMSD between 82 pruned atom pairs is 1.208 angstroms; (across all 167 pairs:
6.224)
> show #!6 models
> hide #!6 models
> show #!18 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!6 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> hide #!3 models
> show #!18 models
> hide #!18 models
> show #!17 models
> show #!16 models
> hide #!16 models
> show #!18 models
> hide #!17 models
> view matrix models
> #1,0.84943,0.0048481,-0.52768,0.65374,-0.36539,0.72688,-0.5815,-14.996,0.38074,0.68675,0.6192,0.19483,#6,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#11,0.3554,0.83707,0.41595,-1.2763,0.68382,0.070534,-0.72623,-14.22,-0.63724,0.54254,-0.54734,0.48453,#2,-0.46068,-0.87689,-0.13724,12.214,-0.014771,-0.14703,0.98902,-16.145,-0.88745,0.45765,0.054778,1.5059,#3,-0.028746,-0.72374,0.68947,11.158,0.45997,-0.62197,-0.6337,-18.381,0.88747,0.29892,0.35078,3.9374,#4,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#5,0.22887,-0.90083,-0.36896,11.233,0.86356,0.36282,-0.35017,-15.736,0.44931,-0.23848,0.86096,4.0367,#7,0.46353,0.81912,0.33791,5.0029,-0.6474,0.57345,-0.50202,-21.729,-0.60499,0.013936,0.79611,6.3283,#8,-0.26206,-0.91936,-0.29342,-0.19912,0.46009,0.14825,-0.87541,-25.028,0.84832,-0.36441,0.38414,-10.304,#9,-0.36876,-0.75997,0.53522,0.42258,-0.57013,0.63969,0.5155,-25.953,-0.73415,-0.11505,-0.66917,-11.957,#10,-0.76439,0.47517,0.4358,-2.938,-0.63904,-0.46854,-0.60999,-30.867,-0.085662,-0.74477,0.6618,-2.3478,#12,0.5306,0.7007,0.47695,28.271,0.79647,-0.60467,0.0022843,-13.278,0.29,0.37867,-0.87893,-22.901,#13,-0.87207,0.20936,-0.44234,-12.953,-0.35472,-0.89312,0.27661,-70.145,-0.33715,0.39813,0.85313,-58.476,#14,0.06735,0.64492,0.76128,-46.484,-0.9052,0.36039,-0.22523,-11.844,-0.41961,-0.67394,0.60805,-31.123,#15,-0.96531,0.14882,-0.21456,-77.459,0.24373,0.21868,-0.94487,-1.6269,-0.093694,-0.96438,-0.24737,25.022,#16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786,#17,0.86185,-0.43699,0.25741,-7.1671,0.16099,0.71702,0.67821,-60.106,-0.48094,-0.54307,0.68831,13.982,#18,-0.37684,0.76002,-0.52949,10.529,0.34458,-0.41558,-0.84176,-4.7032,-0.8598,-0.49966,-0.10528,11.963
> show #1 models
> hide #!6 models
> hide #!18 models
> show #!6 models
> hide #1 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select clear
> show #1 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #4 models
> hide #1 models
> show #!3 models
> hide #4 models
> show #1 models
> hide #!3 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #1 models
> show #1 models
> show #!3 models
> hide #1 models
> hide #!3 models
> show #1 models
> hide #1 models
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> show #!6 models
> hide #!6 models
> color sel & #!18 bychain
> undo
> select clear
> color #!18 bychain
> undo
> show #!3 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!18 models
> hide #!3 models
> show #!6 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!3 models
> hide #!3 models
> show #!18 models
> show #1 models
> hide #!6 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!3 models
> hide #1 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> select ~sel & ##selected
25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected
> ui tool show "Color Actions"
> color sel tan
> color sel goldenrod
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select clear
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> select ~sel & ##selected
25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected
> color sel dark goldenrod
> color sel salmon
> color sel dark goldenrod
> color sel peru
> color sel dark orange
> color sel saddle brown
> color sel dark goldenrod
> color sel slate gray
> color sel steel blue
> color sel cadet blue
> color sel dark olive green
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select clear
> show #1 models
> hide #!3 models
> show #!13 models
> hide #!13 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #4 models
> hide #1 models
> show #1 models
> hide #4 models
> show #4 models
> hide #1 models
> show #!3 models
> hide #!3 models
> show #1 models
> hide #4 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.png width
> 600 height 489 supersample 4 transparentBackground true
> show #4 models
> hide #1 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR-FAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!3 models
> hide #4 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.png
> width 600 height 489 supersample 4 transparentBackground true
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> select clear
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> hide #!3 models
> show #1 models
> show #!6 models
> hide #1 models
> show #1 models
> show #!3 models
> hide #!6 models
> hide #1 models
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.s.png
> width 600 height 489 supersample 4 transparentBackground true
> show #11 models
> hide #!3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #12 models
> hide #12 models
> show #!6 models
> hide #11 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!6 models
> hide #!3 surfaces
> select add #3/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.png
> width 600 height 489 supersample 4 transparentBackground true
> select #3/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/B:124
23 atoms, 23 bonds, 2 residues, 2 models selected
> select add #3/A:148
35 atoms, 35 bonds, 3 residues, 2 models selected
> select add #3/A:184
43 atoms, 42 bonds, 4 residues, 3 models selected
> select add #3/A:101@CA
44 atoms, 42 bonds, 5 residues, 3 models selected
> select add #3/A:102@CB
45 atoms, 43 bonds, 6 residues, 3 models selected
> select subtract #3/A:102
44 atoms, 43 bonds, 5 residues, 3 models selected
> select add #3/A:102
52 atoms, 50 bonds, 6 residues, 3 models selected
> select subtract #3/A:101
51 atoms, 49 bonds, 5 residues, 3 models selected
> select add #3/A:101
59 atoms, 56 bonds, 6 residues, 3 models selected
> select add #3/A:100
73 atoms, 71 bonds, 7 residues, 3 models selected
> select add #3/A:99
81 atoms, 78 bonds, 8 residues, 3 models selected
> select add #3/A:183
91 atoms, 88 bonds, 9 residues, 3 models selected
> select add #3/A:143
97 atoms, 93 bonds, 10 residues, 3 models selected
> select add #3/A:98
104 atoms, 100 bonds, 11 residues, 3 models selected
> select add #3/A:19
110 atoms, 105 bonds, 12 residues, 3 models selected
> select add #3/A:18
118 atoms, 112 bonds, 13 residues, 3 models selected
> select add #3/A:17
124 atoms, 117 bonds, 14 residues, 3 models selected
> select add #3/A:16
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:9
136 atoms, 127 bonds, 16 residues, 3 models selected
> select subtract #3/A:9
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:8
138 atoms, 129 bonds, 16 residues, 3 models selected
> select subtract #3/A:8
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:10@CB
132 atoms, 123 bonds, 16 residues, 3 models selected
> select subtract #3/A:10@CB
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:10
141 atoms, 133 bonds, 16 residues, 3 models selected
> select add #3/B:57
149 atoms, 140 bonds, 17 residues, 3 models selected
> select add #3/B:52
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 148 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select subtract #3/B:52
149 atoms, 140 bonds, 17 residues, 3 models selected
> select add #3/B:52
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CB
158 atoms, 147 bonds, 19 residues, 3 models selected
> label (#!3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #3/B:197
6 atoms, 5 bonds, 1 residue, 1 model selected
> label height 3
> label height 2
> label height 1
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> show #5 models
> hide #!3 models
> select #5/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #5/B:124
23 atoms, 23 bonds, 2 residues, 1 model selected
> select add #5/A:100
37 atoms, 39 bonds, 3 residues, 1 model selected
> select add #5/A:101
45 atoms, 45 bonds, 4 residues, 1 model selected
> select add #5/A:16
52 atoms, 51 bonds, 5 residues, 1 model selected
> select add #5/A:10
62 atoms, 61 bonds, 6 residues, 1 model selected
> select add #5/A:11
69 atoms, 68 bonds, 7 residues, 1 model selected
> select subtract #5/A:11
62 atoms, 61 bonds, 6 residues, 1 model selected
> select add #5/A:12
73 atoms, 72 bonds, 7 residues, 1 model selected
> select add #5/B:60
87 atoms, 87 bonds, 8 residues, 1 model selected
> select add #5/B:57
95 atoms, 94 bonds, 9 residues, 1 model selected
> select add #5/B:58
102 atoms, 100 bonds, 10 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
[Repeated 1 time(s)]
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #5/B:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> show #4 models
> hide #4 models
> show #!3 models
> hide #!5 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!3 models
> hide sel atoms
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> hide #!5 models
> show #7 models
> hide #7 models
> show #11 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select add #11/A:101
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #11/A:143
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #11/A:19
20 atoms, 18 bonds, 3 residues, 1 model selected
> select add #11/A:18
28 atoms, 25 bonds, 4 residues, 1 model selected
> select add #11/A:17
34 atoms, 30 bonds, 5 residues, 1 model selected
> select add #11/A:10
44 atoms, 40 bonds, 6 residues, 1 model selected
> select add #11/A:100
58 atoms, 55 bonds, 7 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_NAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!5 models
> hide #!11 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> ~label #5 residues
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #15 models
> hide #5 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select ::name="CBD"
204 atoms, 224 bonds, 4 residues, 1 model selected
> color sel pale turquoise
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/3w78.AzrC.CBD.FMN.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> select #3/B:126
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #15 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> select #15/B:60
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> select clear
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #15 models
> undo
> hide #!16 models
> show #!16 models
> hide #15 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> show #!6 models
> hide #!16 models
> show #1 models
> hide #!6 models
> show #!16 models
> hide #1 models
> show #!6 models
> hide #!16 models
> show #!16 models
> hide #!6 models
> show #1 models
> hide #!16 models
> show #!16 models
> hide #1 models
> show #!3 models
> hide #!16 models
> show #!16 models
> hide #!3 models
> select #16/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> show #5 models
> hide #5 models
> show #!17 models
> hide #!16 models
> show #1 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #1 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!6 models
> hide #!17 models
> show #15 models
> hide #!3 models
> show #!16 models
> hide #15 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!16 models
> show #!3 models
> show #1 models
> hide #1 models
> show #7 models
> hide #7 models
> hide #!6 models
> show #1 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> hide #1 models
> show #7 models
> show #1 models
> hide #7 models
> show #7 models
> hide #1 models
> show #8 models
> hide #8 models
> show #8 models
> hide #7 models
> view matrix models
> #16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786
> hide #8 models
> show #12 models
> hide #12 models
> show #9 models
> show #10 models
> hide #9 models
> show #!3 models
> hide #10 models
> select #3/A:104
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> view matrix models
> #3,0.23414,-0.80222,0.54921,11.186,0.21867,-0.50698,-0.83376,-19.133,0.94729,0.31531,0.056721,3.3647
> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159
> open 2Bzs fromDatabase pdb format mmcif
Summary of feedback from opening 2Bzs fetched from pdb
---
notes | Fetching compressed mmCIF 2bzs from http://files.rcsb.org/download/2bzs.cif
Fetching CCD CB1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/CB1/CB1.cif
2bzs title:
Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed
by the crystal structure of their complex. [more info...]
Chain information for 2bzs #19
---
Chain | Description | UniProt
A B | NRH DEHYDROGENASE [QUINONE] 2 | NQO2_HUMAN 1-230
Non-standard residues in 2bzs #19
---
CB1 — 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954; Tretazicar)
FAD — flavin-adenine dinucleotide
ZN — zinc ion
> hide #!3 models
> color #!19 bychain
> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159
> show #!3 models
> hide #!3 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> matchmaker #!19 to #3 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2bzs, chain B
(#19), sequence alignment score = 223.4
RMSD between 70 pruned atom pairs is 1.017 angstroms; (across all 198 pairs:
5.647)
> show #!3 models
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #1 models
> hide #!19 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> matchmaker #1 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
> show #!19 models
> hide #1 models
> show #1 models
> hide #!3 models
> hide #!19 models
> show #!19 models
> select #19/B
2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected
> rainbow sel
> hide #1 models
> show #4 models
> hide #4 models
> show #1 models
> select #19/B
2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected
> color sel bychain
> select clear
> hide #1 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #4 models
> hide #!19 models
> show #!19 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #1 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select clear
> open 2VPw fromDatabase pdb format mmcif
Summary of feedback from opening 2VPw fetched from pdb
---
notes | Fetching compressed mmCIF 2vpw from http://files.rcsb.org/download/2vpw.cif
Fetching CCD MGD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MGD/MGD.cif
Fetching CCD MO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/MO/MO.cif
Fetching CCD MQ7 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/MQ7/MQ7.cif
2vpw title:
Polysulfide reductase with bound menaquinone [more info...]
Chain information for 2vpw #20
---
Chain | Description | UniProt
A E | THIOSULFATE REDUCTASE | Q72LA4_THET2 1-765
B F | NRFC PROTEIN | Q72LA5_THET2 1-195
C G | HYPOTHETICAL MEMBRANE SPANNING PROTEIN | Q72LA6_THET2 0-252 1-253
Non-standard residues in 2vpw #20
---
MGD —
2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-
anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide)
MO — molybdenum atom
MQ7 — menaquinone-7
SF4 — iron/sulfur cluster
> hide #!19 models
> hide #1 models
> hide #!20 surfaces
[Repeated 1 time(s)]
> hide #!20 atoms
> show #!20 cartoons
> matchmaker #!20 to #3 & sel
No 'to' model specified
> matchmaker #!20 to #3
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2vpw, chain E
(#20), sequence alignment score = 78
RMSD between 8 pruned atom pairs is 1.398 angstroms; (across all 148 pairs:
20.313)
> show #!3 models
> hide #!3 models
> select /A
51617 atoms, 51746 bonds, 16 pseudobonds, 7421 residues, 24 models selected
> rainbow sel & #!20
> select ::name="MQ7"
30 atoms, 32 bonds, 2 residues, 1 model selected
> show sel surfaces
> open 7NZ1 fromDatabase pdb format mmcif
Summary of feedback from opening 7NZ1 fetched from pdb
---
notes | Fetching compressed mmCIF 7nz1 from http://files.rcsb.org/download/7nz1.cif
Fetching CCD CSX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/CSX/CSX.cif
7nz1 title:
Respiratory complex I from Escherichia coli - focused refinement of
cytoplasmic arm [more info...]
Chain information for 7nz1 #21
---
Chain | Description | UniProt
B | NADH-quinone oxidoreductase subunit B |
D | NADH-quinone oxidoreductase subunit C/D | NUOCD_ECOLI 1-596
E | NADH-quinone oxidoreductase subunit E | NUOE_ECOLI 1-166
F | NADH-quinone oxidoreductase subunit F | NUOF_ECOLI 1-445
G | NADH-quinone oxidoreductase subunit G | NUOG_ECOLI 1-908
I | NADH-quinone oxidoreductase subunit I | NUOI_ECOLI 1-180
Non-standard residues in 7nz1 #21
---
CA — calcium ion
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
SF4 — iron/sulfur cluster
> hide sel atoms
> show sel cartoons
> hide #!20 models
> show #!21 cartoons
> hide #!21 atoms
> view matrix models
> #20,-0.20963,0.97025,0.12114,-159.27,0.41872,0.20104,-0.88558,-19.075,-0.88359,-0.13493,-0.44841,140.58
> color #!21 bychain
> matchmaker #!21 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with 7nz1, chain G
(#21), sequence alignment score = 86.3
RMSD between 22 pruned atom pairs is 0.859 angstroms; (across all 180 pairs:
20.357)
> show #1 models
> select #21/G
7630 atoms, 7235 bonds, 24 pseudobonds, 1469 residues, 2 models selected
> rainbow sel
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!21 models
> show #!21 models
> hide #1 models
> matchmaker #!21 to #8
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_mqo_model_0.cif, chain A (#8) with 7nz1, chain G (#21),
sequence alignment score = 63.6
RMSD between 5 pruned atom pairs is 1.257 angstroms; (across all 362 pairs:
31.062)
> show #8 models
> hide #!21 models
> hide #8 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_4.cif
Chain information for fold_tcr_ankkflltv_model_0.cif #22
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_1.cif #23
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_2.cif #24
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_3.cif #25
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_4.cif #26
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #23-26 to #22
Computing secondary structure
[Repeated 4 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_1.cif, chain B (#23), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.184 angstroms; (across all 111 pairs:
0.184)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_2.cif, chain B (#24), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.232 angstroms; (across all 111 pairs:
0.232)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_3.cif, chain B (#25), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.364 angstroms; (across all 111 pairs:
0.364)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_4.cif, chain B (#26), sequence alignment score =
573.8
RMSD between 110 pruned atom pairs is 0.269 angstroms; (across all 111 pairs:
0.332)
> view matrix models
> #21,0.56571,0.78878,0.24042,-111.9,-0.81332,0.5818,0.0049461,-39.828,-0.13598,-0.19834,0.97066,-77.181
Drag select of 9 atoms, 113 residues, 8 bonds
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_4.cif
Chain information for fold_tcr_demefteae_model_0.cif #27
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_1.cif #28
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_2.cif #29
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_3.cif #30
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_4.cif #31
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
[Repeated 4 time(s)]
> matchmaker #27-31 to #22
Computing secondary structure
[Repeated 5 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_0.cif, chain B (#27), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.323 angstroms; (across all 111 pairs:
0.323)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_1.cif, chain B (#28), sequence alignment score =
570.2
RMSD between 111 pruned atom pairs is 0.204 angstroms; (across all 111 pairs:
0.204)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_2.cif, chain B (#29), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.345 angstroms; (across all 111 pairs:
0.345)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_3.cif, chain B (#30), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.287 angstroms; (across all 111 pairs:
0.287)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_4.cif, chain B (#31), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.349 angstroms; (across all 111 pairs:
0.349)
> select clear
> delete atoms #22-31
> delete bonds #22-31
> show #!13 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
——— End of log from Wed Mar 11 15:25:43 2026 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15H00105LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 216 days, 2 hours, 57 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2718Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
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