id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15914	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070002e1a7000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002d1a4000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002c1a1000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002b19e000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002a19b000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700029198000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700028195000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700027192000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002618f000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002518c000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700024189000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700023186000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700022183000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700021180000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002017d000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001f17a000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001e177000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001d174000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001c171000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001b16e000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001a16b000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700019168000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700018165000 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00007ff85dd9ddc0 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.core._mac_util, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)


{""app_name"":""ChimeraX"",""timestamp"":""2024-09-09 13:16:02.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""2201444A-A859-44A8-95A1-363D5E26CD1A""}
{
  ""uptime"" : 1100000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 502,
  ""deployVersion"" : 210,
  ""modelCode"" : ""iMac20,1"",
  ""coalitionID"" : 3129,
  ""osVersion"" : {
    ""train"" : ""macOS 14.6.1"",
    ""build"" : ""23G93"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2024-09-09 13:16:00.3185 -0500"",
  ""codeSigningMonitor"" : 0,
  ""incident"" : ""2201444A-A859-44A8-95A1-363D5E26CD1A"",
  ""pid"" : 5252,
  ""cpuType"" : ""X86-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2024-09-06 10:46:23.3582 -0500"",
  ""procStartAbsTime"" : 910623989090428,
  ""procExitAbsTime"" : 1178791897092069,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""7DE7F1BA-7E0E-5EF3-8AF1-B22530389684"",""thirdParty"":true},
  ""parentProc"" : ""tcsh"",
  ""parentPid"" : 18570,
  ""coalitionName"" : ""com.apple.Terminal"",
  ""crashReporterKey"" : ""D77CBDCE-560E-A76E-6409-11E87F8970FF"",
  ""responsiblePid"" : 18493,
  ""responsibleProc"" : ""Terminal"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""bridgeVersion"" : {""build"":""21P6074"",""train"":""8.6""},
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0 is not in any region.  Bytes before following region: 4351479808\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1035e5000-1035e9000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"",
  ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000000"",""rawCodes"":[1,0],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000000""},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open alphafold_runs_0p_2p.cxs

Log from Fri Aug 9 15:07:48 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open alphafold_runs_0p_2p.cxs

Log from Thu Aug 8 17:23:41 2024

> alias dd distance delete

> alias rd ui mousemode right distance

> alias rs ui mousemode right select

> alias nmr1 hide #1.2-20 models

> alias slall label sel text
> ""{0.label_one_letter_code}{0.number}{0.insertion_code}""

> alias lmearo label #1:thr,met,ala,leu,val,ile,phe,tyr text
> ""{0.label_one_letter_code}{0.number}{0.insertion_code}""

> alias showbb show #1@N,C,CA,O,H; cartoon #1 suppress false; transparency #1
> 50 target c; hide #1:hoh

> alias hidebb hide #1@N,C,CA,O,H target a; transparency $1 0 target c

> alias sdist ui tool show Distances

> alias showmet show #1:ile,leu,val,met,ala,thr target a; hide H; color #1:ile
> paleturquoise target a; color #1:leu lightsalmon target a; color #1:val
> khaki target a; color #1:met thistle target a; color #1:ala yellowgreen
> target ab; color #1:thr aquamarine target a;color byhetero target a ; style
> #1 ball

> alias showmet2 show #2:ile,leu,val,met,ala,thr target a; hide H; color
> #2:ile paleturquoise target a; color #2:leu lightsalmon target a; color
> #2:val khaki target a; color #2:met thistle target a; color #2:ala
> yellowgreen target ab; color #2:thr aquamarine target a;color byhetero
> target a ; style #2 ball

> alias showmet3 show #3:ile,leu,val,met,ala,thr target a; hide H; color
> #3:ile paleturquoise target a; color #3:leu lightsalmon target a; color
> #3:val khaki target a; color #3:met thistle target a; color #3:ala
> yellowgreen target ab; color #3:thr aquamarine target a;color byhetero
> target a ; style #3 ball

> alias showaro show #1:phe,tyr,his,trp target ab; hide H; color #1:phe plum
> target a; color #1:tyr lightpink target a; color byhetero target a

> ui mousemode right distance

> alias fgfr1_brake show #1: 546,562,638

> alias fgfr2_brake show #1: 549,565,641

> alias fgfr3_brake show #1: 540,556,632

> alias fgfr4_brake show #1: 535,551,627

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open fold_kd_ctail_0p_run_1_model_0.cif

Chain information for fold_kd_ctail_0p_run_1_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_4.cif

Chain information for fold_kd_ctail_0p_run_1_model_1.cif #2  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_1_model_2.cif #3  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_1_model_3.cif #4  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_1_model_4.cif #5  
---  
Chain | Description  
A | .  
  

> 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_1.cif, chain A (#2), sequence alignment score =
1871  
RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs:
4.590)  
  

> 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_2.cif, chain A (#3), sequence alignment score =
1887.8  
RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs:
21.274)  
  

> matchmaker #4 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_3.cif, chain A (#4), sequence alignment score =
1881.8  
RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs:
8.985)  
  

> matchmaker #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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_4.cif, chain A (#5), sequence alignment score =
1871  
RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs:
24.527)  
  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_4.cif

Chain information for fold_kd_ctail_0p_run_2_model_0.cif #6  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_1.cif #7  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_2.cif #8  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_3.cif #9  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_4.cif #10  
---  
Chain | Description  
A | .  
  

> 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_0.cif, chain A (#6), sequence alignment score =
1887.8  
RMSD between 365 pruned atom pairs is 0.000 angstroms; (across all 365 pairs:
0.000)  
  

> matchmaker #7 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_1.cif, chain A (#7), sequence alignment score =
1871  
RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs:
4.590)  
  

> matchmaker #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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_2.cif, chain A (#8), sequence alignment score =
1887.8  
RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs:
21.274)  
  

> matchmaker #9 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_3.cif, chain A (#9), sequence alignment score =
1881.8  
RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs:
8.985)  
  

> matchmaker #10 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_4.cif, chain A (#10), sequence alignment score =
1871  
RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs:
24.527)  
  

> open /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_4.cif

Chain information for fold_kd_ctail_2p_model_0.cif #11  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_1.cif #12  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_2.cif #13  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_3.cif #14  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_4.cif #15  
---  
Chain | Description  
A | .  
  

> matchmaker #1? to #1

Missing or invalid ""matchAtoms"" argument: only initial part ""#1"" of atom
specifier valid  

> matchmaker #11 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_0.cif, chain A (#11), sequence alignment score = 1833.8  
RMSD between 272 pruned atom pairs is 0.401 angstroms; (across all 365 pairs:
28.856)  
  

> matchmaker #12 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_1.cif, chain A (#12), sequence alignment score = 1833.8  
RMSD between 273 pruned atom pairs is 0.368 angstroms; (across all 365 pairs:
31.133)  
  

> matchmaker #13 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_2.cif, chain A (#13), sequence alignment score = 1842.8  
RMSD between 265 pruned atom pairs is 0.376 angstroms; (across all 365 pairs:
27.667)  
  

> matchmaker #14 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_3.cif, chain A (#14), sequence alignment score = 1842.8  
RMSD between 271 pruned atom pairs is 0.446 angstroms; (across all 365 pairs:
28.883)  
  

> matchmaker #15 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_4.cif, chain A (#15), sequence alignment score = 1833.8  
RMSD between 269 pruned atom pairs is 0.368 angstroms; (across all 365 pairs:
28.340)  
  

> matchmaker #16 to #1

No molecules/chains to match specified  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_4.cif

Chain information for fold_kd_ctail_2p_run_2_model_0.cif #16  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_1.cif #17  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_2.cif #18  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_3.cif #19  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_4.cif #20  
---  
Chain | Description  
A | .  
  

> matchmaker #16 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_0.cif, chain A (#16), sequence alignment score =
1821.8  
RMSD between 269 pruned atom pairs is 0.342 angstroms; (across all 365 pairs:
29.041)  
  

> matchmaker #17 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_1.cif, chain A (#17), sequence alignment score =
1821.8  
RMSD between 270 pruned atom pairs is 0.304 angstroms; (across all 365 pairs:
34.580)  
  

> matchmaker #18 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_2.cif, chain A (#18), sequence alignment score =
1827.8  
RMSD between 269 pruned atom pairs is 0.331 angstroms; (across all 365 pairs:
29.393)  
  

> matchmaker #19 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_3.cif, chain A (#19), sequence alignment score =
1863.8  
RMSD between 278 pruned atom pairs is 0.415 angstroms; (across all 365 pairs:
13.710)  
  

> matchmaker #20 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_4.cif, chain A (#20), sequence alignment score =
1833.8  
RMSD between 271 pruned atom pairs is 0.330 angstroms; (across all 365 pairs:
29.597)  
  

> ui tool show ""Renumber Residues""

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458

7300 residues renumbered  

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458

0 residues renumbered  

> show :771

> hide #1-10 target m

> show #1-10 target m

> hide #11-20 target m

> show :653,654

> show #11-20 target m

> hide #1-10 target m

> show #1-10 target m

> hide #1-10 target m

> hide :780-822

> hide :780-822 cartoons

> show #1-10 target m

> show :695-725 atoms

> show :767-779 atoms

> hide #1-10 target m

> show #1-10 target m

> hide #1-10 target m

> hide #11-19 target m

> color #20:767-779 green target c

> color #20:767-779 byelement target a

> show :694 atoms

> distance #20/A:694@CE1 #20/A:767@CD1

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU
767 CD1: 6.998Å  

> distance #20/A:694@CE1 #20/A:767@CD2

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU
767 CD2: 6.279Å  

> distance #20/A:696@CD1 #20/A:769@CD1

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU
769 CD1: 2.824Å  

> distance #20/A:696@CD1 #20/A:769@CD2

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU
769 CD2: 4.764Å  

> ~distance #20/A:696@CD1 #20/A:769@CD2

> distance #20/A:695@CG2 #20/A:773@CD2

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU
773 CD2: 5.040Å  

> ~distance #20/A:695@CG2 #20/A:773@CD2

> distance #20/A:695@CG2 #20/A:773@CD1

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU
773 CD1: 6.542Å  

> ~distance #20/A:695@CG2 #20/A:773@CD1

> hide :780-822 cartoons

> hide :766-822 cartoons

> distance #20/A:724@ND2 #20/A:768@O

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and ASP
768 O: 3.574Å  

> distance #20/A:724@ND2 #20/A:767@O

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and LEU
767 O: 5.063Å  

> hide :766-822 atoms

> save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD-
> Ctail/alphafold_runs_0p_2p.pdb

> save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD-
> Ctail/alphafold_runs_0p_2p.cxs

——— End of log from Thu Aug 8 17:23:41 2024 ———

opened ChimeraX session  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_4.cif

Chain information for fold_kd_ctail_y653p_run_1_model_0.cif #22  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_1.cif #23  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_2.cif #24  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_3.cif #25  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_4.cif #26  
---  
Chain | Description  
A | .  
  

> matchmaker #22-26 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_0.cif, chain A (#22), sequence alignment score
= 1869.8  
RMSD between 281 pruned atom pairs is 0.444 angstroms; (across all 365 pairs:
16.950)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_1.cif, chain A (#23), sequence alignment score
= 1827.8  
RMSD between 269 pruned atom pairs is 0.326 angstroms; (across all 365 pairs:
25.654)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_2.cif, chain A (#24), sequence alignment score
= 1833.8  
RMSD between 268 pruned atom pairs is 0.334 angstroms; (across all 365 pairs:
27.277)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_3.cif, chain A (#25), sequence alignment score
= 1827.8  
RMSD between 269 pruned atom pairs is 0.345 angstroms; (across all 365 pairs:
28.333)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_4.cif, chain A (#26), sequence alignment score
= 1830.8  
RMSD between 270 pruned atom pairs is 0.353 angstroms; (across all 365 pairs:
27.133)  
  

> show #11-20 target m

> hide :780-822 cartoons

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_4.cif

Chain information for fold_kd_ctail_y653p_run_2_model_0.cif #27  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_1.cif #28  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_2.cif #29  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_3.cif #30  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_4.cif #31  
---  
Chain | Description  
A | .  
  

> matchmaker #27-31 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_0.cif, chain A (#27), sequence alignment score
= 1827.8  
RMSD between 268 pruned atom pairs is 0.409 angstroms; (across all 365 pairs:
31.267)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_1.cif, chain A (#28), sequence alignment score
= 1842.8  
RMSD between 273 pruned atom pairs is 0.458 angstroms; (across all 365 pairs:
31.317)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_2.cif, chain A (#29), sequence alignment score
= 1833.8  
RMSD between 268 pruned atom pairs is 0.382 angstroms; (across all 365 pairs:
29.220)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_3.cif, chain A (#30), sequence alignment score
= 1836.8  
RMSD between 266 pruned atom pairs is 0.366 angstroms; (across all 365 pairs:
28.088)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_4.cif, chain A (#31), sequence alignment score
= 1833.8  
RMSD between 272 pruned atom pairs is 0.691 angstroms; (across all 365 pairs:
30.898)  
  

> ui tool show ""Renumber Residues""

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A
> #26/A #27/A #28/A #29/A #30/A #31/A seqStart 458

3650 residues renumbered  

> hide :780-822 cartoons

> show :766-780 cartoons

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_4.cif

Chain information for fold_kd_ctail_y654p_run_1_model_0.cif #32  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_1.cif #33  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_2.cif #34  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_3.cif #35  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_4.cif #36  
---  
Chain | Description  
A | .  
  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_4.cif

Chain information for fold_kd_ctail_y654p_run_2_model_0.cif #37  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_1.cif #38  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_2.cif #39  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_3.cif #40  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_4.cif #41  
---  
Chain | Description  
A | .  
  

> matchmaker #32-41 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_0.cif, chain A (#32), sequence alignment score
= 1830.8  
RMSD between 274 pruned atom pairs is 0.339 angstroms; (across all 365 pairs:
30.830)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_1.cif, chain A (#33), sequence alignment score
= 1833.8  
RMSD between 273 pruned atom pairs is 0.367 angstroms; (across all 365 pairs:
29.517)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_2.cif, chain A (#34), sequence alignment score
= 1833.8  
RMSD between 275 pruned atom pairs is 0.503 angstroms; (across all 365 pairs:
33.883)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_3.cif, chain A (#35), sequence alignment score
= 1833.8  
RMSD between 272 pruned atom pairs is 0.398 angstroms; (across all 365 pairs:
28.779)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_4.cif, chain A (#36), sequence alignment score
= 1842.8  
RMSD between 265 pruned atom pairs is 0.443 angstroms; (across all 365 pairs:
28.961)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_0.cif, chain A (#37), sequence alignment score
= 1827.8  
RMSD between 274 pruned atom pairs is 0.440 angstroms; (across all 365 pairs:
30.375)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_1.cif, chain A (#38), sequence alignment score
= 1833.8  
RMSD between 272 pruned atom pairs is 0.466 angstroms; (across all 365 pairs:
31.050)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_2.cif, chain A (#39), sequence alignment score
= 1833.8  
RMSD between 274 pruned atom pairs is 0.336 angstroms; (across all 365 pairs:
29.924)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_3.cif, chain A (#40), sequence alignment score
= 1833.8  
RMSD between 271 pruned atom pairs is 0.449 angstroms; (across all 365 pairs:
28.353)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_4.cif, chain A (#41), sequence alignment score
= 1833.8  
RMSD between 270 pruned atom pairs is 0.399 angstroms; (across all 365 pairs:
32.127)  
  

> hide :780-822 cartoons

> ui tool show ""Renumber Residues""

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A
> #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A
> #38/A #39/A #40/A #41/A seqStart 458

3650 residues renumbered  

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A
> #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A
> #38/A #39/A #40/A #41/A seqStart 458

0 residues renumbered  

> hide :780-822 cartoons

> hide cartoons

> hide atoms

> show :695-725 cartoons

> show #1-10 target m

> show :695-725 atoms

> hide #1-10 target m

> coulombic #41:720

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2 -fi
mol2 -o
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2);
atoms read (36), bonds read (36).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) ``  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `Info: Total number of electrons: 166; net charge: -2`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PTR) ``  
Charges for residue PTR determined  
Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface
#41.1: minimum, -14.09, mean -2.42, maximum 12.27  

> coulombic #41:695-725

Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface
#41.1: minimum, -14.09, mean -2.42, maximum 12.27  

> show :766-780 cartoons

> hide #!41 models

> show #!41 models

> hide #!41 models

> coulombic #40:766-780

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2 -fi
mol2 -o
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2);
atoms read (34), bonds read (34).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) ``  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `Info: Total number of electrons: 164; net charge: -2`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PTR) ``  
Charges for residue PTR determined  
Coulombic values for fold_kd_ctail_y654p_run_2_model_3.cif_A SES surface
#40.1: minimum, -13.70, mean -2.40, maximum 12.19  

> show #!41 models

> coulombic #41:766-780

Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface
#41.1: minimum, -14.09, mean -2.42, maximum 12.27  

> hide #11-20,22-39#!40-41 surfaces

> show :458-780 cartoons

> show #1-10 target m

> show :653,654 atoms

> hide #1-10 target m

> hide #11-20 target m

> show #11-20 target m

> hide #22-31 target m

> hide #32-39#!40-41 target m

> show #11-20 target m

> show #22-39#!40 target m

> hide #12 models

> show #12 models

> hide #11 models

> show #11 models

> hide #14 models

> show #14 models

> hide #16 models

> show #16 models

> hide #22 models

> hide #19 models

> hide #12-39#!40-41 target m

> show #1-10 target m

> hide #1-10 target m

> save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD-
> Ctail/alphafold_runs_0p_2p.cxs

——— End of log from Fri Aug 9 15:07:48 2024 ———

opened ChimeraX session  

> open
> /Users/ksinha01/Kinases_local/FGFR1/FGFR1_struc_calc/fgfr1_03132024_v2/CNS/fgfr1_03132024_v2.pdb
> format pdb

Chain information for fgfr1_03132024_v2.pdb  
---  
Chain | Description  
42.1/A 42.2/A 42.3/A 42.4/A 42.5/A 42.6/A 42.7/A 42.8/A 42.9/A 42.10/A 42.11/A 42.12/A 42.13/A 42.14/A 42.15/A 42.16/A 42.17/A 42.18/A 42.19/A 42.20/A | No description available  
  

> matchmaker #42 to #11

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_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.1), sequence alignment score = 1439.2  
RMSD between 151 pruned atom pairs is 1.266 angstroms; (across all 308 pairs:
6.495)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.2), sequence alignment score = 1419.4  
RMSD between 124 pruned atom pairs is 1.241 angstroms; (across all 308 pairs:
6.760)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.3), sequence alignment score = 1427.8  
RMSD between 115 pruned atom pairs is 1.181 angstroms; (across all 308 pairs:
6.912)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.4), sequence alignment score = 1450.6  
RMSD between 137 pruned atom pairs is 1.186 angstroms; (across all 308 pairs:
6.559)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.5), sequence alignment score = 1407.4  
RMSD between 117 pruned atom pairs is 1.105 angstroms; (across all 308 pairs:
6.707)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.6), sequence alignment score = 1434.4  
RMSD between 135 pruned atom pairs is 1.197 angstroms; (across all 308 pairs:
6.156)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.7), sequence alignment score = 1429  
RMSD between 122 pruned atom pairs is 1.182 angstroms; (across all 308 pairs:
6.646)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.8), sequence alignment score = 1461.4  
RMSD between 145 pruned atom pairs is 1.283 angstroms; (across all 308 pairs:
5.989)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.9), sequence alignment score = 1472.2  
RMSD between 135 pruned atom pairs is 1.226 angstroms; (across all 308 pairs:
6.411)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.10), sequence alignment score = 1446.4  
RMSD between 119 pruned atom pairs is 1.157 angstroms; (across all 308 pairs:
7.135)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.11), sequence alignment score = 1454.2  
RMSD between 143 pruned atom pairs is 1.194 angstroms; (across all 308 pairs:
6.046)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.12), sequence alignment score = 1447.6  
RMSD between 151 pruned atom pairs is 1.130 angstroms; (across all 308 pairs:
5.664)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.13), sequence alignment score = 1468.6  
RMSD between 156 pruned atom pairs is 1.230 angstroms; (across all 308 pairs:
6.473)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.14), sequence alignment score = 1451.2  
RMSD between 163 pruned atom pairs is 1.280 angstroms; (across all 308 pairs:
6.365)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.15), sequence alignment score = 1460.8  
RMSD between 133 pruned atom pairs is 1.216 angstroms; (across all 308 pairs:
6.593)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.16), sequence alignment score = 1412.2  
RMSD between 139 pruned atom pairs is 1.256 angstroms; (across all 308 pairs:
5.993)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.17), sequence alignment score = 1441  
RMSD between 123 pruned atom pairs is 1.130 angstroms; (across all 308 pairs:
6.606)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.18), sequence alignment score = 1460.2  
RMSD between 125 pruned atom pairs is 1.189 angstroms; (across all 308 pairs:
6.819)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.19), sequence alignment score = 1429  
RMSD between 151 pruned atom pairs is 1.320 angstroms; (across all 308 pairs:
6.077)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fgfr1_03132024_v2.pdb, chain A (#42.20), sequence alignment score = 1442.2  
RMSD between 146 pruned atom pairs is 1.244 angstroms; (across all 308 pairs:
6.551)  
  

> hide #42.2-20 target m

> show : 672,537

> hide atoms

> show : 672,537

> color #42.1:MET yellow target c

> show : 672,537,651

> hide #11 models

> show : 672,537,651,667

> show : 672,537,651,667,645

> show : 672,537,651,667,645,644

> show : 534,538

> show : 534,538,544

> show : 534,538,544,601

> show : 534,538,544,601,757

> show #1 models

> hide #1 models

Alignment identifier is 1  
Alignment identifier is 2  

> select
> #42.1/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.2/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.3/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.4/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.5/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.6/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.7/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.8/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.9/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.10/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.11/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.12/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.13/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.14/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.15/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.16/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.17/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.18/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.19/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763
> #42.20/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763

42140 atoms, 42300 bonds, 2540 residues, 20 models selected  

> show : 534,538,544,601,757,662,706

> show : 534,538,544,601,757,662,706,693

> open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_0.cif

Chain information for fold_fgfr1_kd_2p_model_0.cif #43  
---  
Chain | Description  
A | .  
  

> open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_1.cif

Chain information for fold_fgfr1_kd_2p_model_1.cif #44  
---  
Chain | Description  
A | .  
  

> open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_2.cif

Chain information for fold_fgfr1_kd_2p_model_2.cif #45  
---  
Chain | Description  
A | .  
  

> open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_3.cif

Chain information for fold_fgfr1_kd_2p_model_3.cif #46  
---  
Chain | Description  
A | .  
  

> open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_4.cif

Chain information for fold_fgfr1_kd_2p_model_4.cif #47  
---  
Chain | Description  
A | .  
  

> matchmaker #43-47 to #11

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_kd_ctail_2p_model_0.cif, chain A (#11) with
fold_fgfr1_kd_2p_model_0.cif, chain A (#43), sequence alignment score = 1563.4  
RMSD between 291 pruned atom pairs is 0.589 angstroms; (across all 308 pairs:
1.618)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fold_fgfr1_kd_2p_model_1.cif, chain A (#44), sequence alignment score = 1557.4  
RMSD between 290 pruned atom pairs is 0.385 angstroms; (across all 308 pairs:
1.566)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fold_fgfr1_kd_2p_model_2.cif, chain A (#45), sequence alignment score = 1572.4  
RMSD between 292 pruned atom pairs is 0.392 angstroms; (across all 308 pairs:
1.447)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fold_fgfr1_kd_2p_model_3.cif, chain A (#46), sequence alignment score = 1572.4  
RMSD between 291 pruned atom pairs is 0.530 angstroms; (across all 308 pairs:
1.480)  
  
Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with
fold_fgfr1_kd_2p_model_4.cif, chain A (#47), sequence alignment score = 1574.2  
RMSD between 274 pruned atom pairs is 0.643 angstroms; (across all 308 pairs:
1.389)  
  

> hide #!42 models

> show : 534,538,544,601,757,662,706,693

> show : 534,538,544,601,757,662,706,693 atoms

> show #!42 models

> hide #!42 models

> ui tool show ""Renumber Residues""

> renumber #43/A #44/A #45/A #46/A #47/A seqStart 458

1540 residues renumbered  

> renumber #43/A #44/A #45/A #46/A #47/A seqStart 458

0 residues renumbered  

> show : 534,538,544,601,757,662,706,693 atoms

> style #43-47 ball

Changed 12285 atom styles  

> hide #44-47 target m

> hide atoms

> show #43: 672,651

> show #!42 models

> show #42.1: 672,651

> hide #!42 models

> show #42.1: 672,651,653,654

> show #43: 672,651,653,654

> show #!42 models

> hide #43 models

> show #43: 672,651,653,654,706

> show #42.1: 672,651,653,654,706

> hide atoms

> close #1-10

> show #43 models

> hide #43 models

> show #43 models

> hide #!42 models

> rename #43 id #1

> rename #44 id #2

> rename #45 id #3

> rename #46 id #4

> rename #47 id #5

> showmet

Changed 2457 atom styles  

> distance #1/A:672@CD2 #1/A:713@CD1

Distance between fold_fgfr1_kd_2p_model_0.cif #1/A LEU 672 CD2 and LEU 713
CD1: 3.824Å  

> show #!21 models

> select add #21

42140 atoms, 42300 bonds, 6 pseudobonds, 2540 residues, 22 models selected  

> show #21.1 models

> show #!42 models

> hide #1 models

> show #42.1:672,651,667

> open 3gqi

3gqi title:  
Crystal Structure of activated receptor tyrosine kinase in complex with
substrates [more info...]  
  
Chain information for 3gqi #6  
---  
Chain | Description | UniProt  
A | Basic fibroblast growth factor receptor 1 | FGFR1_HUMAN 458-774  
B | Phospholipase C-gamma-1 | PLCG1_RAT 545-770  
  
Non-standard residues in 3gqi #6  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
DVT — decavanadate  
MG — magnesium ion  
  

> hide #42.1 models

> show #42.1 models

> matchmaker #6 to #42.1

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 fgfr1_03132024_v2.pdb, chain A (#42.1) with 3gqi, chain A (#6),
sequence alignment score = 1449.6  
RMSD between 133 pruned atom pairs is 1.191 angstroms; (across all 302 pairs:
6.924)  
  

> hide #!42 models

> show #!42 models

> hide #6/B cartoons

> select up

67248 atoms, 67891 bonds, 6 pseudobonds, 4122 residues, 22 models selected  

> select up

98240 atoms, 99340 bonds, 6 pseudobonds, 6160 residues, 22 models selected  

> select down

67248 atoms, 67891 bonds, 6 pseudobonds, 4122 residues, 22 models selected  

> select down

42140 atoms, 42300 bonds, 6 pseudobonds, 2540 residues, 22 models selected  

> select down

42140 atoms, 42300 bonds, 6 pseudobonds, 2540 residues, 22 models selected  

> show #6/A:672,651,667

> hide #!42 models

> hide atoms

> show #6/A:672,651,667

> style #!6 ball

Changed 4369 atom styles  

> label #6/A:672,651,667


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open alphafold_runs_0p_2p.cxs

Log from Fri Aug 9 15:07:48 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open alphafold_runs_0p_2p.cxs

Log from Thu Aug 8 17:23:41 2024

> alias dd distance delete

> alias rd ui mousemode right distance

> alias rs ui mousemode right select

> alias nmr1 hide #1.2-20 models

> alias slall label sel text
> ""{0.label_one_letter_code}{0.number}{0.insertion_code}""

> alias lmearo label #1:thr,met,ala,leu,val,ile,phe,tyr text
> ""{0.label_one_letter_code}{0.number}{0.insertion_code}""

> alias showbb show #1@N,C,CA,O,H; cartoon #1 suppress false; transparency #1
> 50 target c; hide #1:hoh

> alias hidebb hide #1@N,C,CA,O,H target a; transparency $1 0 target c

> alias sdist ui tool show Distances

> alias showmet show #1:ile,leu,val,met,ala,thr target a; hide H; color #1:ile
> paleturquoise target a; color #1:leu lightsalmon target a; color #1:val
> khaki target a; color #1:met thistle target a; color #1:ala yellowgreen
> target ab; color #1:thr aquamarine target a;color byhetero target a ; style
> #1 ball

> alias showmet2 show #2:ile,leu,val,met,ala,thr target a; hide H; color
> #2:ile paleturquoise target a; color #2:leu lightsalmon target a; color
> #2:val khaki target a; color #2:met thistle target a; color #2:ala
> yellowgreen target ab; color #2:thr aquamarine target a;color byhetero
> target a ; style #2 ball

> alias showmet3 show #3:ile,leu,val,met,ala,thr target a; hide H; color
> #3:ile paleturquoise target a; color #3:leu lightsalmon target a; color
> #3:val khaki target a; color #3:met thistle target a; color #3:ala
> yellowgreen target ab; color #3:thr aquamarine target a;color byhetero
> target a ; style #3 ball

> alias showaro show #1:phe,tyr,his,trp target ab; hide H; color #1:phe plum
> target a; color #1:tyr lightpink target a; color byhetero target a

> ui mousemode right distance

> alias fgfr1_brake show #1: 546,562,638

> alias fgfr2_brake show #1: 549,565,641

> alias fgfr3_brake show #1: 540,556,632

> alias fgfr4_brake show #1: 535,551,627

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open fold_kd_ctail_0p_run_1_model_0.cif

Chain information for fold_kd_ctail_0p_run_1_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_4.cif

Chain information for fold_kd_ctail_0p_run_1_model_1.cif #2  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_1_model_2.cif #3  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_1_model_3.cif #4  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_1_model_4.cif #5  
---  
Chain | Description  
A | .  
  

> 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_1.cif, chain A (#2), sequence alignment score =
1871  
RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs:
4.590)  
  

> 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_2.cif, chain A (#3), sequence alignment score =
1887.8  
RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs:
21.274)  
  

> matchmaker #4 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_3.cif, chain A (#4), sequence alignment score =
1881.8  
RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs:
8.985)  
  

> matchmaker #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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_1_model_4.cif, chain A (#5), sequence alignment score =
1871  
RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs:
24.527)  
  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_4.cif

Chain information for fold_kd_ctail_0p_run_2_model_0.cif #6  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_1.cif #7  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_2.cif #8  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_3.cif #9  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_0p_run_2_model_4.cif #10  
---  
Chain | Description  
A | .  
  

> 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_0.cif, chain A (#6), sequence alignment score =
1887.8  
RMSD between 365 pruned atom pairs is 0.000 angstroms; (across all 365 pairs:
0.000)  
  

> matchmaker #7 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_1.cif, chain A (#7), sequence alignment score =
1871  
RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs:
4.590)  
  

> matchmaker #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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_2.cif, chain A (#8), sequence alignment score =
1887.8  
RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs:
21.274)  
  

> matchmaker #9 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_3.cif, chain A (#9), sequence alignment score =
1881.8  
RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs:
8.985)  
  

> matchmaker #10 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_0p_run_2_model_4.cif, chain A (#10), sequence alignment score =
1871  
RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs:
24.527)  
  

> open /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_4.cif

Chain information for fold_kd_ctail_2p_model_0.cif #11  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_1.cif #12  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_2.cif #13  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_3.cif #14  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_model_4.cif #15  
---  
Chain | Description  
A | .  
  

> matchmaker #1? to #1

Missing or invalid ""matchAtoms"" argument: only initial part ""#1"" of atom
specifier valid  

> matchmaker #11 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_0.cif, chain A (#11), sequence alignment score = 1833.8  
RMSD between 272 pruned atom pairs is 0.401 angstroms; (across all 365 pairs:
28.856)  
  

> matchmaker #12 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_1.cif, chain A (#12), sequence alignment score = 1833.8  
RMSD between 273 pruned atom pairs is 0.368 angstroms; (across all 365 pairs:
31.133)  
  

> matchmaker #13 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_2.cif, chain A (#13), sequence alignment score = 1842.8  
RMSD between 265 pruned atom pairs is 0.376 angstroms; (across all 365 pairs:
27.667)  
  

> matchmaker #14 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_3.cif, chain A (#14), sequence alignment score = 1842.8  
RMSD between 271 pruned atom pairs is 0.446 angstroms; (across all 365 pairs:
28.883)  
  

> matchmaker #15 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_model_4.cif, chain A (#15), sequence alignment score = 1833.8  
RMSD between 269 pruned atom pairs is 0.368 angstroms; (across all 365 pairs:
28.340)  
  

> matchmaker #16 to #1

No molecules/chains to match specified  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_4.cif

Chain information for fold_kd_ctail_2p_run_2_model_0.cif #16  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_1.cif #17  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_2.cif #18  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_3.cif #19  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_2p_run_2_model_4.cif #20  
---  
Chain | Description  
A | .  
  

> matchmaker #16 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_0.cif, chain A (#16), sequence alignment score =
1821.8  
RMSD between 269 pruned atom pairs is 0.342 angstroms; (across all 365 pairs:
29.041)  
  

> matchmaker #17 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_1.cif, chain A (#17), sequence alignment score =
1821.8  
RMSD between 270 pruned atom pairs is 0.304 angstroms; (across all 365 pairs:
34.580)  
  

> matchmaker #18 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_2.cif, chain A (#18), sequence alignment score =
1827.8  
RMSD between 269 pruned atom pairs is 0.331 angstroms; (across all 365 pairs:
29.393)  
  

> matchmaker #19 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_3.cif, chain A (#19), sequence alignment score =
1863.8  
RMSD between 278 pruned atom pairs is 0.415 angstroms; (across all 365 pairs:
13.710)  
  

> matchmaker #20 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_2p_run_2_model_4.cif, chain A (#20), sequence alignment score =
1833.8  
RMSD between 271 pruned atom pairs is 0.330 angstroms; (across all 365 pairs:
29.597)  
  

> ui tool show ""Renumber Residues""

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458

7300 residues renumbered  

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458

0 residues renumbered  

> show :771

> hide #1-10 target m

> show #1-10 target m

> hide #11-20 target m

> show :653,654

> show #11-20 target m

> hide #1-10 target m

> show #1-10 target m

> hide #1-10 target m

> hide :780-822

> hide :780-822 cartoons

> show #1-10 target m

> show :695-725 atoms

> show :767-779 atoms

> hide #1-10 target m

> show #1-10 target m

> hide #1-10 target m

> hide #11-19 target m

> color #20:767-779 green target c

> color #20:767-779 byelement target a

> show :694 atoms

> distance #20/A:694@CE1 #20/A:767@CD1

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU
767 CD1: 6.998Å  

> distance #20/A:694@CE1 #20/A:767@CD2

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU
767 CD2: 6.279Å  

> distance #20/A:696@CD1 #20/A:769@CD1

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU
769 CD1: 2.824Å  

> distance #20/A:696@CD1 #20/A:769@CD2

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU
769 CD2: 4.764Å  

> ~distance #20/A:696@CD1 #20/A:769@CD2

> distance #20/A:695@CG2 #20/A:773@CD2

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU
773 CD2: 5.040Å  

> ~distance #20/A:695@CG2 #20/A:773@CD2

> distance #20/A:695@CG2 #20/A:773@CD1

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU
773 CD1: 6.542Å  

> ~distance #20/A:695@CG2 #20/A:773@CD1

> hide :780-822 cartoons

> hide :766-822 cartoons

> distance #20/A:724@ND2 #20/A:768@O

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and ASP
768 O: 3.574Å  

> distance #20/A:724@ND2 #20/A:767@O

Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and LEU
767 O: 5.063Å  

> hide :766-822 atoms

> save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD-
> Ctail/alphafold_runs_0p_2p.pdb

> save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD-
> Ctail/alphafold_runs_0p_2p.cxs

——— End of log from Thu Aug 8 17:23:41 2024 ———

opened ChimeraX session  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_4.cif

Chain information for fold_kd_ctail_y653p_run_1_model_0.cif #22  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_1.cif #23  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_2.cif #24  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_3.cif #25  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_1_model_4.cif #26  
---  
Chain | Description  
A | .  
  

> matchmaker #22-26 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_0.cif, chain A (#22), sequence alignment score
= 1869.8  
RMSD between 281 pruned atom pairs is 0.444 angstroms; (across all 365 pairs:
16.950)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_1.cif, chain A (#23), sequence alignment score
= 1827.8  
RMSD between 269 pruned atom pairs is 0.326 angstroms; (across all 365 pairs:
25.654)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_2.cif, chain A (#24), sequence alignment score
= 1833.8  
RMSD between 268 pruned atom pairs is 0.334 angstroms; (across all 365 pairs:
27.277)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_3.cif, chain A (#25), sequence alignment score
= 1827.8  
RMSD between 269 pruned atom pairs is 0.345 angstroms; (across all 365 pairs:
28.333)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_1_model_4.cif, chain A (#26), sequence alignment score
= 1830.8  
RMSD between 270 pruned atom pairs is 0.353 angstroms; (across all 365 pairs:
27.133)  
  

> show #11-20 target m

> hide :780-822 cartoons

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_4.cif

Chain information for fold_kd_ctail_y653p_run_2_model_0.cif #27  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_1.cif #28  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_2.cif #29  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_3.cif #30  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y653p_run_2_model_4.cif #31  
---  
Chain | Description  
A | .  
  

> matchmaker #27-31 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_0.cif, chain A (#27), sequence alignment score
= 1827.8  
RMSD between 268 pruned atom pairs is 0.409 angstroms; (across all 365 pairs:
31.267)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_1.cif, chain A (#28), sequence alignment score
= 1842.8  
RMSD between 273 pruned atom pairs is 0.458 angstroms; (across all 365 pairs:
31.317)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_2.cif, chain A (#29), sequence alignment score
= 1833.8  
RMSD between 268 pruned atom pairs is 0.382 angstroms; (across all 365 pairs:
29.220)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_3.cif, chain A (#30), sequence alignment score
= 1836.8  
RMSD between 266 pruned atom pairs is 0.366 angstroms; (across all 365 pairs:
28.088)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y653p_run_2_model_4.cif, chain A (#31), sequence alignment score
= 1833.8  
RMSD between 272 pruned atom pairs is 0.691 angstroms; (across all 365 pairs:
30.898)  
  

> ui tool show ""Renumber Residues""

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A
> #26/A #27/A #28/A #29/A #30/A #31/A seqStart 458

3650 residues renumbered  

> hide :780-822 cartoons

> show :766-780 cartoons

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_4.cif

Chain information for fold_kd_ctail_y654p_run_1_model_0.cif #32  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_1.cif #33  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_2.cif #34  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_3.cif #35  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_1_model_4.cif #36  
---  
Chain | Description  
A | .  
  

> open
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_0.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_1.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_2.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_3.cif
> /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_4.cif

Chain information for fold_kd_ctail_y654p_run_2_model_0.cif #37  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_1.cif #38  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_2.cif #39  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_3.cif #40  
---  
Chain | Description  
A | .  
  
Chain information for fold_kd_ctail_y654p_run_2_model_4.cif #41  
---  
Chain | Description  
A | .  
  

> matchmaker #32-41 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_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_0.cif, chain A (#32), sequence alignment score
= 1830.8  
RMSD between 274 pruned atom pairs is 0.339 angstroms; (across all 365 pairs:
30.830)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_1.cif, chain A (#33), sequence alignment score
= 1833.8  
RMSD between 273 pruned atom pairs is 0.367 angstroms; (across all 365 pairs:
29.517)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_2.cif, chain A (#34), sequence alignment score
= 1833.8  
RMSD between 275 pruned atom pairs is 0.503 angstroms; (across all 365 pairs:
33.883)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_3.cif, chain A (#35), sequence alignment score
= 1833.8  
RMSD between 272 pruned atom pairs is 0.398 angstroms; (across all 365 pairs:
28.779)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_1_model_4.cif, chain A (#36), sequence alignment score
= 1842.8  
RMSD between 265 pruned atom pairs is 0.443 angstroms; (across all 365 pairs:
28.961)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_0.cif, chain A (#37), sequence alignment score
= 1827.8  
RMSD between 274 pruned atom pairs is 0.440 angstroms; (across all 365 pairs:
30.375)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_1.cif, chain A (#38), sequence alignment score
= 1833.8  
RMSD between 272 pruned atom pairs is 0.466 angstroms; (across all 365 pairs:
31.050)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_2.cif, chain A (#39), sequence alignment score
= 1833.8  
RMSD between 274 pruned atom pairs is 0.336 angstroms; (across all 365 pairs:
29.924)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_3.cif, chain A (#40), sequence alignment score
= 1833.8  
RMSD between 271 pruned atom pairs is 0.449 angstroms; (across all 365 pairs:
28.353)  
  
Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with
fold_kd_ctail_y654p_run_2_model_4.cif, chain A (#41), sequence alignment score
= 1833.8  
RMSD between 270 pruned atom pairs is 0.399 angstroms; (across all 365 pairs:
32.127)  
  

> hide :780-822 cartoons

> ui tool show ""Renumber Residues""

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A
> #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A
> #38/A #39/A #40/A #41/A seqStart 458

3650 residues renumbered  

> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A
> #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A
> #38/A #39/A #40/A #41/A seqStart 458

0 residues renumbered  

> hide :780-822 cartoons

> hide cartoons

> hide atoms

> show :695-725 cartoons

> show #1-10 target m

> show :695-725 atoms

> hide #1-10 target m

> coulombic #41:720

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2 -fi
mol2 -o
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2);
atoms read (36), bonds read (36).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) ``  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `Info: Total number of electrons: 166; net charge: -2`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PTR) ``  
Charges for residue PTR determined  
Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface
#41.1: minimum, -14.09, mean -2.42, maximum 12.27  

> coulombic #41:695-725

Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface
#41.1: minimum, -14.09, mean -2.42, maximum 12.27  

> show :766-780 cartoons

> hide #!41 models

> show #!41 models

> hide #!41 models

> coulombic #40:766-780

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2 -fi
mol2 -o
/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2);
atoms read (34), bonds read (34).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) ``  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `Info: Total number of electrons: 164; net charge: -2`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(PTR) ``  
(PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(PTR) ``  
(PTR) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PTR) ``  
Charges for residue PTR determined  
Coulombic values for fold_kd_ctail_y654p_run_2_model_3.cif_A SES surface
#40.1: minimum, -13.70, mean -2.40, maximum 12.19  

> show #!41 models

> coulombic #41:766-780

Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface
#41.1: minimum, -14.09, mean -2.42, maximum 12.27  

> hide #11-20,22-39#!40-41 surfaces

> show :458-780 cartoons

> show #1-10 target m

> show :653,654 atoms

> hide #1-10 target m

> hide #11-20 target m

> show #11-20 target m

> hide #22-31 target m

> hide #32-39#!40-41 target m

> show #11-20 target m

> show #22-39#!40 target m

> hide #12 models

> show #12 models

> hide #11 models

> show #11 models

> hide #14 models

> show #14 models

> hide #16 models

> show #16 models

> hide #22 models

> hide #19 models

> hide #12-39#!40-41 target m

> show #1-10 target m

> hide #1-10 target m

> save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD-
> Ctail/alphafold_runs_0p_2p.cxs

——— End of log from Fri Aug 9 15:07:48 2024 ———

opened ChimeraX session  

> label #6/A:672,651,667

> label #6/A:672,651,667,671,668

> label #11:672,651,667,671,668




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 10-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache (per Core): 256 KB
      L3 Cache: 20 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 580.140.1~8

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 13 days, 15 hours, 48 minutes

Graphics/Displays:

    AMD Radeon Pro 5300:

      Chipset Model: AMD Radeon Pro 5300
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0047
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XL-012
      Option ROM Version: 113-D322A1XL-012
      EFI Driver Version: 01.01.231
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG Ultra HD:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.4
    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: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    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: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	assigned	normal		Window Toolkit								all	ChimeraX