﻿id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20165	ChimeraX bug report submission	a.fasemire@…		"{{{
The following bug report has been submitted:
Platform:        macOS-15.7.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Bus error

Thread 0x000000030e1b3000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000030d1a7000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000030c19b000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000030b18f000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000030a183000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000309177000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000030816b000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000030715f000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000306153000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000305147000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000030413b000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001fd0fe240 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 65)


{""app_name"":""ChimeraX"",""timestamp"":""2026-04-14 16:29:33.00 +0200"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.7.4 (24G517)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""B01646FE-C090-4B14-81A6-3C24F6613E26""}
{
  ""uptime"" : 1200000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""Mac15,12"",
  ""coalitionID"" : 952,
  ""osVersion"" : {
    ""train"" : ""macOS 15.7.4"",
    ""build"" : ""24G517"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2026-04-14 16:29:27.1768 +0200"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""B01646FE-C090-4B14-81A6-3C24F6613E26"",
  ""pid"" : 91401,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2026-04-11 17:26:23.3477 +0200"",
  ""procStartAbsTime"" : 27258919118470,
  ""procExitAbsTime"" : 30022829721765,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""1285D59A-DC79-5D40-B366-2F3C3C4E451C"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""31E19731-CFC0-05F8-DC37-45557C23533F"",
  ""appleIntelligenceStatus"" : {""state"":""available""},
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""codeSigningAuxiliaryInfo"" : 0,
  ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""},
  ""bootSessionUUID"" : ""EC65655E-BA96-4622-B5B0-4D24C1466F0D"",
  ""wakeTime"" : 4,
  ""sleepWakeUUID"" : ""2A0B5A11-0BDE-424C-9805-0376F79A3B8B"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0x39a9c7bb28 is in 0x1000000000-0x7000000000;  bytes after start: 178942098216  bytes before end: 233374762199\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)         fc0000000-1000000000   [  1.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GPU Carveout (reserved)    1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n      GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  "",
  ""exception"" : {""codes"":""0x0000000000000002, 0x00000039a9c7bb28"",""rawCodes"":[2,247661574952],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGBUS"",""subtype"":""KERN_PROTECTION_FAILURE at 0x00000039a9c7bb28""},
  ""termination"" : {""flags"":0,""code"":10,""namespace"":""SIGNAL"",""indicator"":""Bus error: 10"",""byProc"":""ChimeraX"",""byPid"":91401},
  ""ktriageinfo"" : ""CL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3bcc001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n"",
  ""vmregioninfo"" : ""0x39a9c7bb28 is in 0x1000000000-0x7000000000;  bytes after start: 178942098216  bytes before end: 233374762199\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)         fc0000000-1000000000   [  1.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GPU Carveout (reserved)    1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n      GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  "",
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  ""faultingThread"" : 0,
  ""threads"" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Probac1_Figures/figures_prep.cxs""

Opened ClpP_volume_map_1_95A_bfactor_77_flip.mrc as #9, grid size 256,256,256,
pixel 0.84, shown at level 0.042, step 1, values float32  
Log from Thu Apr 9 16:14:06 2026UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/ayomidefasemire/Downloads/ClpP structures comparison .cxs""

Log from Sun Mar 22 14:55:57 2026 Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle  
Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with
that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Majka/Downloads/16Mar26_flip_KHS_QMR_refined.pdb

Chain information for 16Mar26_flip_KHS_QMR_refined.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
  

> hide surfaces

> select add #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> hide sel surfaces

> show sel atoms

[Repeated 2 time(s)]

> show sel cartoons

[Repeated 1 time(s)]

> hide sel surfaces

> style sel sphere

Changed 41972 atom styles  

> style sel sphere

Changed 41972 atom styles  

> style sel stick

Changed 41972 atom styles  

> select subtract #1

Nothing selected  

> ui tool show ""Show Sequence Viewer""

[Repeated 1 time(s)]

> sequence chain /A

Alignment identifier is 1/A  

> open 6NB1 fromDatabase pdb format mmcif

Summary of feedback from opening 6NB1 fetched from pdb  
---  
note | Fetching compressed mmCIF 6nb1 from http://files.rcsb.org/download/6nb1.cif  
  
6nb1 title:  
Crystal structure of Escherichia coli ClpP protease complexed with small
molecule activator, ACP1-06 [more info...]  
  
Chain information for 6nb1 #2  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI 1-207 2-207  
  
Non-standard residues in 6nb1 #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
KHS —
N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  

> open 1TYF fromDatabase pdb format mmcif

Summary of feedback from opening 1TYF fetched from pdb  
---  
note | Fetching compressed mmCIF 1tyf from http://files.rcsb.org/download/1tyf.cif  
  
1tyf title:  
The structure of CLPP At 2.3 angstrom resolution suggests A model for atp-
dependent proteolysis [more info...]  
  
Chain information for 1tyf #3  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N | CLP PEPTIDASE | CLPP_ECOLI 1-193  
  

> ui tool show Matchmaker

> matchmaker #3#!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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J
(#3), sequence alignment score = 937.6  
RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs:
2.425)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  

> select add #3

21308 atoms, 20384 bonds, 3808 residues, 1 model selected  

> style sel stick

Changed 21308 atom styles  

> hide sel surfaces

> show sel atoms

> hide #!2 models

> select subtract #3

Nothing selected  

> show #!2 models

> hide surfaces

> show atoms

> select add #2

21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected  

> hide sel surfaces

> show sel atoms

> style sel stick

Changed 21442 atom styles  

> select subtract #2

Nothing selected  

> hide #3 models

> show #3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #3 models

> hide #!1 atoms

> show #!1 cartoons

> show #!2 models

> select add #2

21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected  

> hide sel atoms

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show sel cartoons

> select subtract #2

Nothing selected  

> open 1YG6 fromDatabase pdb format mmcif

Summary of feedback from opening 1YG6 fetched from pdb  
---  
note | Fetching compressed mmCIF 1yg6 from http://files.rcsb.org/download/1yg6.cif  
  
1yg6 title:  
ClpP [more info...]  
  
Chain information for 1yg6 #4  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI 1-193  
  
Non-standard residues in 1yg6 #4  
---  
MPD — (4S)-2-methyl-2,4-pentanediol  
  

> ui tool show Matchmaker

> matchmaker #3-4#!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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J
(#3), sequence alignment score = 937.6  
RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs:
2.425)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1yg6, chain I
(#4), sequence alignment score = 934.6  
RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs:
2.818)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  

> select add #4

21540 atoms, 20901 bonds, 3585 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> style sel stick

Changed 21540 atom styles  

> hide sel atoms

> show sel cartoons

> select subtract #4

Nothing selected  

> show #3 models

> hide atoms

> show cartoons

> color #1 #ff55ffff

> color #2 #55007fff

> color #3 #ffaaffff

> color #4 #aaaaffff

> hide #!2 models

> hide #!1 models

> hide #3 models

> hide #4 models

> show #!1 models

> show #!2 models

> show #3 models

> show #4 models

> open 3MT6 fromDatabase pdb format mmcif

Summary of feedback from opening 3MT6 fetched from pdb  
---  
note | Fetching compressed mmCIF 3mt6 from http://files.rcsb.org/download/3mt6.cif  
  
3mt6 title:  
Structure of ClpP from Escherichia coli in complex with ADEP1 [more info...]  
  
Chain information for 3mt6 #5  
---  
Chain | Description | UniProt  
1 2 3 4 c d e f g h i j k l m n o p q r s t u v w x y z | ACYLDEPSIPEPTIDE 1 |   
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI -13-193  
  
Non-standard residues in 3mt6 #5  
---  
MAA — N-methyl-L-alanine  
MP8 — (4R)-4-methyl-L-proline  
MPD — (4S)-2-methyl-2,4-pentanediol  
OTT — (2E,4E,6E)-octa-2,4,6-trienoic acid (2,4,6-octatrienoic acid)  
  
3mt6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #3-4#!2,5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J
(#3), sequence alignment score = 937.6  
RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs:
2.425)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1yg6, chain I
(#4), sequence alignment score = 934.6  
RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs:
2.818)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 3mt6, chain E
(#5), sequence alignment score = 954.4  
RMSD between 181 pruned atom pairs is 0.466 angstroms; (across all 186 pairs:
0.661)  
  

> select add #5

46272 atoms, 43362 bonds, 19 pseudobonds, 9074 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> hide sel surfaces

> select subtract #5

Nothing selected  

> select add #5

46272 atoms, 43362 bonds, 19 pseudobonds, 9074 residues, 2 models selected  

> select #5/O

1613 atoms, 1511 bonds, 314 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> hide #3 models

> hide #4 models

> hide #!1 models

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> save ""C:/Users/Majka/Downloads/ClpP structures comparison .cxs""

> show #4 models

> show #3 models

> hide #4 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> select #5/1

52 atoms, 55 bonds, 7 residues, 1 model selected  

> select #2/N

1516 atoms, 1467 bonds, 1 pseudobond, 254 residues, 2 models selected  

> style sel stick

Changed 1516 atom styles  

> show sel atoms

> undo

[Repeated 2 time(s)]

> select #5/V

1548 atoms, 1461 bonds, 1 pseudobond, 293 residues, 2 models selected  

> undo

> select ::name=""KHS""

1064 atoms, 1092 bonds, 28 residues, 2 models selected  

> show sel atoms

> save ""C:/Users/Majka/Downloads/ClpP structures comparison .cxs""

——— End of log from Sun Mar 22 14:55:57 2026 ———

opened ChimeraX session  

> set bgColor white

> select add #2

22100 atoms, 21511 bonds, 12 pseudobonds, 3526 residues, 3 models selected  

> select add #1

63414 atoms, 63147 bonds, 26 pseudobonds, 6158 residues, 4 models selected  

> select subtract #1

21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected  

> select subtract #2

Nothing selected  

> show #4 models

> hide #!2 models

> hide #!5 models

> set bgColor black

> hide #3 models

> show #3 models

> hide #3 models

> hide #4 models

> show #3 models

> hide #!1 models

> show #!2 models

> hide #3 models

> set bgColor white

> show #3 models

> show #4 models

> hide #3 models

> show #3 models

> hide #4 models

> show #4 models

> hide #4 models

> show #!5 models

> hide #!2 models

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Map/ClpP_volume_map_1_95A_bfactor_77_flip.mrc""

Opened ClpP_volume_map_1_95A_bfactor_77_flip.mrc as #6, grid size 256,256,256,
pixel 0.84, shown at level 0.0426, step 1, values float32  

> volume #6 level 0.037

> ui tool show ""Segment Map""

Segmenting ClpP_volume_map_1_95A_bfactor_77_flip.mrc, density threshold
0.037000  
Only showing 60 of 174 regions.  
Showing 60 of 174 region surfaces  
2757 watershed regions, grouped to 174 regions  
Showing ClpP_volume_map_1_95A_bfactor_77_flip.seg - 174 regions, 60 surfaces  
Smoothing and grouping, standard deviation 5 voxels  
Only showing 60 of 100 regions.  
Showing 60 of 100 region surfaces  
Got 100 regions after smoothing 5 voxels.  

> show #!1 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #3 models

> hide #!5 models

> hide #!1 models

> show #!2 models

> show #!6 models

> show #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> close #7

> show #!1 models

> select #1/A:75

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:75-76

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select #1/A:75

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:75

19 atoms, 18 bonds, 1 residue, 1 model selected  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A #1/B #1/C #1/D #1/E #1/F #1/G #1/H #1/I #1/J #1/K #1/L
> #1/M #1/N

Alignment identifier is 1  

> select #1/A-N:75

266 atoms, 252 bonds, 14 residues, 1 model selected  

> select #1/A-N:75

266 atoms, 252 bonds, 14 residues, 1 model selected  

> select #1/A-N:58

224 atoms, 210 bonds, 14 residues, 1 model selected  

> select #1/A-N:58

224 atoms, 210 bonds, 14 residues, 1 model selected  

> select #1/A-N:83

224 atoms, 210 bonds, 14 residues, 1 model selected  

> select #1/A-N:83

224 atoms, 210 bonds, 14 residues, 1 model selected  

> select #1/A-N:42

224 atoms, 210 bonds, 14 residues, 1 model selected  

> select #1/A-N:42

224 atoms, 210 bonds, 14 residues, 1 model selected  

> select #1/A-N:28

210 atoms, 196 bonds, 14 residues, 1 model selected  

> select #1/A-N:28

210 atoms, 196 bonds, 14 residues, 1 model selected  

> select #1/A-N:32

168 atoms, 154 bonds, 14 residues, 1 model selected  

> select #1/A-N:32

168 atoms, 154 bonds, 14 residues, 1 model selected  

> select add #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> select subtract #1

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #3 models

> hide #!1 models

> show #!1 models

> hide #3 models

> show #!5 models

> hide #!5 models

> show #!6 models

> select #1/I,J,K,L,M

14990 atoms, 15110 bonds, 5 pseudobonds, 945 residues, 2 models selected  

> color zone #1 near sel distance 5.0 color forestgreen

Expected a keyword  

> color zone #1 near sel distance 5.0 forestgreen

Expected a keyword  

> color zone #6 near sel distance 5.0 farColor forestgreen

> color zone #6 near sel distance 3.0 farColor forestgreen

> ui tool show ""Color Actions""

> color sel cornflower blue

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> color zone #6 near sel & #1 distance 5.04

> select #1/A,B,C,D,E,F,G

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color zone #6 near sel & #1 distance 5.04

> ui tool show ""Color Actions""

> color sel deep sky blue

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color sel cyan

> select clear

> color zone #6 near #1 distance 5.04

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light gray

> select #1/A,B,C,D,E,F,G

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel dim gray

> select clear

> color zone #6 near #1 distance 5.04

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel dark gray

> select clear

> color zone #6 near #1 distance 5.04

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel lavender

> select #1/A,B,C,D,E,F,G

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color sel indigo

> select clear

> color zone #6 near #1 distance 5.04

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel orchid

> select clear

> color zone #6 near #1 distance 5.04

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color sel light steel blue

> select clear

> color zone #6 near #1 distance 5.04

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color sel pale turquoise

> select clear

> color zone #6 near #1 distance 5.04

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color sel light slate gray

> select clear

> color zone #6 near #1 distance 5.04

> select ::name=""KHS""

1064 atoms, 1092 bonds, 28 residues, 2 models selected  

> color sel teal

> color sel green

> select clear

> color zone #6 near #1 distance 5.04

> select clear

> select #1/A-N:16

252 atoms, 238 bonds, 14 residues, 1 model selected  

> select #1/A-N:16-22

1610 atoms, 1610 bonds, 98 residues, 1 model selected  

> hide #!6 models

> select #1/A-N:35

154 atoms, 140 bonds, 14 residues, 1 model selected  

> select #1/A-N:16-35

3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected  

> color sel magenta

> show #!6 models

> select clear

> color zone #6 near #1 distance 5.04

> select #1/A-N:16-35

3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected  

> volume style surface

> hide #!6 models

> surface sel

> show #!6 models

> color surface magenta

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel magenta

> transparency (#!1 & sel) 80

> select clear

[Repeated 1 time(s)]

> select ::name=""KHS""

1064 atoms, 1092 bonds, 28 residues, 2 models selected  

> color sel dark goldenrod

> select clear

> color zone #6 near #1 distance 5.04

> open 6nb1 structureFactors true

Summary of feedback from opening 6nb1 fetched from pdb  
---  
notes | Fetching compressed 6nb1 structure factors from http://files.rcsb.org/download/6nb1-sf.cif  
Resolution: 1.9000085448470343  
Launching live xmap mgr took 1.6232528686523438 seconds.  
  
Opened (LIVE) 2mFo-DFc as #7.1.1.2, grid size 50,38,40, pixel
0.589,0.632,0.621, shown at level 0.705, step 1, values float32  
Opened (LIVE) mFo-DFc as #7.1.1.3, grid size 50,38,40, pixel
0.589,0.632,0.621, shown at level -0.203,0.203, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_17 as #7.1.1.4, grid size 50,38,40, pixel
0.589,0.632,0.621, shown at level 0.206, step 1, values float32  
6nb1 title:  
Crystal structure of Escherichia coli ClpP protease complexed with small
molecule activator, ACP1-06 [more info...]  
  
Chain information for 6nb1  
---  
Chain | Description | UniProt  
7.2/A 7.2/B 7.2/C 7.2/D 7.2/E 7.2/F 7.2/G 7.2/H 7.2/I 7.2/J 7.2/K 7.2/L 7.2/M 7.2/N | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI 1-207 2-207  
  
Non-standard residues in 6nb1 #7.2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
KHS —
N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide  
  
406 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!7.1 models

> show #!7.1 models

> hide #!7.2 models

> show #!7.2 models

> hide #!7.2 models

> show #!7.2 models

> hide #!7.2 models

> show #!7.2 models

> hide #7.3 models

> close #7

Deleting Crystallographic maps(6nb1-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_17  

> hide #!6 models

> select add #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> show surfaces sel

Expected ',' or a keyword  

> show sel surfaces

> select ::name=""KHS""

1064 atoms, 1092 bonds, 28 residues, 2 models selected  

> show sel & #!1 atoms

> hide sel & #!1 atoms

> show sel & #!1 atoms

> style sel & #!1 sphere

Changed 658 atom styles  

> select clear

> select #1/A-N:16-35

3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected  

> transparency (#!1 & sel) 60

> select clear

> show #3 models

> hide #!1 models

> select add #3

21308 atoms, 20384 bonds, 3808 residues, 1 model selected  

> show sel surfaces

> hide sel atoms

> undo

[Repeated 2 time(s)]

> show #!3 cartoons

> select add #3

21308 atoms, 20384 bonds, 3808 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> surface hidePatches (#!3 & sel)

> select clear

> select #3/H,I,J,K,L,M,N

10653 atoms, 10192 bonds, 1903 residues, 1 model selected  

> color sel indigo

> select #3/A,B,C,D,E,F,G

10655 atoms, 10192 bonds, 1905 residues, 1 model selected  

> color sel light slate gray

> select #3/A-N:16-35

2352 atoms, 2380 bonds, 280 residues, 1 model selected  

> color sel magenta

> ui tool show ""Show Sequence Viewer""

> sequence chain #3/A #3/B #3/C #3/D #3/E #3/F #3/G #3/H #3/I #3/J #3/K #3/L
> #3/M #3/N #4/A #4/B #4/C #4/D #4/E #4/F #4/G #4/H #4/I #4/J #4/K #4/L #4/M
> #4/N

Alignment identifier is 2  

> select #3/A-N:19 #4/A-N:19

224 atoms, 196 bonds, 28 residues, 2 models selected  

> select #3/A-N:11-19
> #4/A,D-F:1-19/B,G:2-19/C:5-19/H:8-19/I-J:10-19/K:16-19/L-M:12-19/N:17-19

2499 atoms, 2505 bonds, 308 residues, 2 models selected  
CLP PEPTIDASE [ID: 2] region 28 chains [1-19] RMSD: 1.096  
  

> select clear

> select #3/A,B,C,D,E,F,G

10655 atoms, 10192 bonds, 1905 residues, 1 model selected  

> color sel light slate gray

> select #3/H,I,J,K,L,M,N

10653 atoms, 10192 bonds, 1903 residues, 1 model selected  

> color sel indigo

> select clear

> ui tool show ""Show Sequence Viewer""

> sequence chain #3/A #3/B #3/C #3/D #3/E #3/F #3/G #3/H #3/I #3/J #3/K #3/L
> #3/M #3/N #4/A #4/B #4/C #4/D #4/E #4/F #4/G #4/H #4/I #4/J #4/K #4/L #4/M
> #4/N

Alignment identifier is 2  

> select #3/A-N:19 #4/A-N:19

224 atoms, 196 bonds, 28 residues, 2 models selected  

> select #3/A-N:11-19
> #4/A,D-F:1-19/B,G:2-19/C:5-19/H:8-19/I-J:10-19/K:16-19/L-M:12-19/N:17-19

2499 atoms, 2505 bonds, 308 residues, 2 models selected  
CLP PEPTIDASE [ID: 2] region 28 chains [1-19] RMSD: 1.096  
  

> color sel magenta

> select clear

> select add #3

21308 atoms, 20384 bonds, 3808 residues, 1 model selected  

> surface (#!3 & sel)

> select clear

> select #3/A-N:1-19

1036 atoms, 1036 bonds, 126 residues, 1 model selected  

> transparency (#!3 & sel) 70

> select clear

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!3 models

> cd ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Probac1_Figures""

Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main
Project/ClpP/Probac1_Figures  

> save 1TYF_1 width 2000 supersample 4

Cannot determine format for '1TYF_1'  

> save 1TYF_1.png width 2000 supersample 4

> save 1TYF_2.png width 2000 supersample 4

> show #!1 models

> hide #!3 models

> save data_1.png width 2000 supersample 4

> save data_2.png width 2000 supersample 4

[Repeated 1 time(s)]

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> select #3/A-N:1-19

1036 atoms, 1036 bonds, 126 residues, 1 model selected  

> transparency (#!3 & sel) 0

> select clear

> save 1TYF_3.png width 2000 supersample 4

> show #!1 models

> hide #!3 models

> select #1/A-N:16-35

3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected  

> transparency (#!1 & sel) 0

> select clear

> save data_3.png width 2000 supersample 4

> save data_4.png width 2000 supersample 4

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/docking/ClpP_DHFR_Probac1/clpP_DHFR_PRBC_frank.pdb""

Chain information for clpP_DHFR_PRBC_frank.pdb #7  
---  
Chain | Description  
A B | No description available  
H | No description available  
I | No description available  
  
Computing secondary structure  

> select #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> surface hidePatches (#!1 & sel)

> select ::name=""KHS""

1064 atoms, 1092 bonds, 28 residues, 2 models selected  

> style sel & #!1 stick

Changed 658 atom styles  

> select clear

> hide #!1 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #7 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with
clpP_DHFR_PRBC_frank.pdb, chain I (#7), sequence alignment score = 881.1  
RMSD between 176 pruned atom pairs is 0.362 angstroms; (across all 176 pairs:
0.362)  
  

> select ::name=""PRB""

69 atoms, 72 bonds, 1 residue, 1 model selected  

> color sel light sea green

> select clear

> hide #7 models

> show #!6 models

> hide #!1 models

> show #!1 models

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Map/test_asymmetric_map.mrc""

Opened test_asymmetric_map.mrc as #8, grid size 256,256,256, pixel 0.84, shown
at level 0.0428, step 1, values float32  

> hide #!6 models

> hide #!1 models

> show #!6 models

> hide #!8 models

> show #!8 models

> fitmap #6 inMap #8

Fit map ClpP_volume_map_1_95A_bfactor_77_flip.mrc in map
test_asymmetric_map.mrc using 195735 points  
correlation = 0.9974, correlation about mean = 0.9758, overlap = 894.8  
steps = 152, shift = 1.67, angle = 17.7 degrees  
  
Position of ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#6) relative to
test_asymmetric_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.96361098 -0.23397631 -0.12926315 41.50325809  
0.25065052 0.95892918 0.13277476 -37.24829245  
0.09288806 -0.16034310 0.98268098 9.90778098  
Axis -0.48179659 -0.36514900 0.79657909  
Axis point 171.62206310 153.77425141 0.00000000  
Rotation angle (degrees) 17.70959179  
Shift along axis 1.49737967  
  

> hide #!6 models

> show #!1 models

> fitmap #1 inMap #8

Fit molecule 16Mar26_flip_KHS_QMR_refined.pdb (#1) to map
test_asymmetric_map.mrc (#8) using 41972 atoms  
average map value = 0.05091, steps = 148  
shifted from previous position = 1.68  
rotated from previous position = 17.7 degrees  
atoms outside contour = 19244, contour level = 0.042842  
  
Position of 16Mar26_flip_KHS_QMR_refined.pdb (#1) relative to
test_asymmetric_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.96361310 -0.23401205 -0.12918263 41.49555884  
0.25065054 0.95896209 0.13253685 -37.23739034  
0.09286603 -0.16009394 0.98272368 9.88457216  
Axis -0.48118856 -0.36512657 0.79695681  
Axis point 171.54046910 153.74748158 0.00000000  
Rotation angle (degrees) 17.70226995  
Shift along axis 1.50674939  
  

> show #!6 models

> hide #!1 models

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/28Mar_flip_KHS_QMR_refined.pdb""

Chain information for 28Mar_flip_KHS_QMR_refined.pdb #9  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
  

> hide #!9 models

> show #!9 models

> select add #9

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select clear

Must specify one map, got 0  

> fitmap #9 inMap #8

Fit molecule 28Mar_flip_KHS_QMR_refined.pdb (#9) to map
test_asymmetric_map.mrc (#8) using 41972 atoms  
average map value = 0.05091, steps = 148  
shifted from previous position = 1.68  
rotated from previous position = 17.7 degrees  
atoms outside contour = 19251, contour level = 0.042842  
  
Position of 28Mar_flip_KHS_QMR_refined.pdb (#9) relative to
test_asymmetric_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.96361171 -0.23400654 -0.12920295 41.49833440  
0.25064935 0.95896094 0.13254739 -37.23776800  
0.09288363 -0.16010885 0.98271959 9.88275255  
Axis -0.48121400 -0.36517646 0.79691859  
Axis point 171.54789170 153.75638342 0.00000000  
Rotation angle (degrees) 17.70289406  
Shift along axis 1.50452585  
  

> undo

[Repeated 2 time(s)]

> close #9

> close #6

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/28Mar_flip_KHS_QMR_refined.pdb""

Chain information for 28Mar_flip_KHS_QMR_refined.pdb #6  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
  

> hide #!6 atoms

> show #!6 cartoons

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Map/ClpP_volume_map_1_95A_bfactor_77_flip.mrc""

Opened ClpP_volume_map_1_95A_bfactor_77_flip.mrc as #9, grid size 256,256,256,
pixel 0.84, shown at level 0.0426, step 1, values float32  

> hide #!6 models

> fitmap #8 inMap #9

Fit map test_asymmetric_map.mrc in map
ClpP_volume_map_1_95A_bfactor_77_flip.mrc using 167708 points  
correlation = 0.9987, correlation about mean = 0.982, overlap = 849.7  
steps = 136, shift = 1.67, angle = 17.7 degrees  
  
Position of test_asymmetric_map.mrc (#8) relative to
ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) coordinates:  
Matrix rotation and translation  
0.96361431 0.25061912 0.09293821 -31.57671855  
-0.23396910 0.95897005 -0.16010905 46.99198765  
-0.12925135 0.13253870 0.98271440 0.59004779  
Axis 0.48121617 0.36535804 -0.79683405  
Axis point 171.53066021 153.78511267 0.00000000  
Rotation angle (degrees) 17.70228062  
Shift along axis 1.50350289  
  

> show #!6 models

> volume #9 level 0.042

> hide #!9 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!8 models

> select add #8

2 models selected  

> hide #!6 models

No model chosen to save relative to  

> save ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Map/ClpP_asym_shift_2_17_flip.mrc"" models #8

> select clear

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Map/ClpP_asym_shift_2_17_flip.mrc""

Opened ClpP_asym_shift_2_17_flip.mrc as #10, grid size 256,256,256, pixel
0.84, shown at level 0.0428, step 1, values float32  

> close #10

> select add #8

2 models selected  

> show #!6 models

> close #8

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Map/test_asymmetric_map.mrc""

Opened test_asymmetric_map.mrc as #8, grid size 256,256,256, pixel 0.84, shown
at level 0.0428, step 1, values float32  

> fitmap #6 inMap #8

Fit molecule 28Mar_flip_KHS_QMR_refined.pdb (#6) to map
test_asymmetric_map.mrc (#8) using 41972 atoms  
average map value = 0.05091, steps = 148  
shifted from previous position = 1.68  
rotated from previous position = 17.7 degrees  
atoms outside contour = 19251, contour level = 0.042842  
  
Position of 28Mar_flip_KHS_QMR_refined.pdb (#6) relative to
test_asymmetric_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.96361171 -0.23400654 -0.12920295 41.49833440  
0.25064935 0.95896094 0.13254739 -37.23776800  
0.09288363 -0.16010885 0.98271959 9.88275255  
Axis -0.48121400 -0.36517646 0.79691859  
Axis point 171.54789170 153.75638342 0.00000000  
Rotation angle (degrees) 17.70289406  
Shift along axis 1.50452585  
  

> select add #6

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> save ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/28Mar_Final_shift_asym.pdb"" selectedOnly true

> close #6

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/28Mar_Final_shift_asym.pdb""

Chain information for 28Mar_Final_shift_asym.pdb #6  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
  

> hide #!6 atoms

> show #!6 cartoons

Computing secondary structure  

> hide #!8 models

> hide #!6 models

> show #!8 models

> open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic
> Models/Pdb/28Mar_flip_KHS_QMR_refined.pdb""

Chain information for 28Mar_flip_KHS_QMR_refined.pdb #10  
---  
Chain | Description  
A B C D E F G H I J K L M N | No description available  
  

> hide #!10 atoms

> show #!10 cartoons

> hide #!10 models

> show #!6 models

> select ::name=""KHS""

2380 atoms, 2436 bonds, 56 residues, 4 models selected  

> show sel & #!6 atoms

> select clear

> close #8

> hide #!6 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> select #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> show surfaces sel

Expected ',' or a keyword  

> surface sel

> hide sel atoms

> show sel atoms

> hide sel surfaces

> hide sel atoms

> select ::name=""KHS""

2380 atoms, 2436 bonds, 56 residues, 4 models selected  

> show sel & #!1 atoms

> select clear

> select #1/A-N:16-35

3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected  

> color sel light steel blue

> color sel light slate gray

> select clear

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> select #1/A,B,C,D,E,F,G

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> color sel indigo

> select clear

> select add #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> surface (#!1 & sel)

> select #1/H,I,J,K,L,M,N

20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected  

> select #1/H-N:16-35

1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected  

> color sel light steel blue

> color sel light blue

> color sel light slate gray

> color sel slate gray

> color sel steel blue

> color sel dark slate blue

> color sel light gray

> color sel dark slate gray

> color sel steel blue

> color sel teal

> color sel medium aquamarine

> color sel dark cyan

> color sel cornflower blue

> color sel light sea green

> color sel medium turquoise

> color sel royal blue

> color sel medium purple

> color sel dark orchid

> color sel dark magenta

> color sel purple

> color sel medium purple

> color sel pale violet red

> color sel midnight blue

> color sel dark slate gray

> color sel gainsboro

> color sel light cyan

> color sel violet

> color sel alice blue

> color sel honeydew

> color sel azure

> color sel wheat

> color sel beige

> color sel white smoke

> color sel mint cream

> color sel ghost white

> color sel antique white

> color sel gray

> color sel dim gray

> color sel dark gray

> color sel burly wood

> color sel light coral

> color sel aquamarine

> color sel powder blue

> color sel silver

> color sel light gray

> color sel thistle

> color sel dark olive green

> color sel dark slate gray

> color sel midnight blue

> color sel pale violet red

> color sel medium purple

> color sel light gray

> color sel gray

> color sel dark gray

> color sel dim gray

> color sel dark slate gray

> color sel midnight blue

> color sel pale violet red

> color sel medium purple

> color sel slate gray

> color sel light slate gray

> color sel cadet blue

> color sel steel blue

> color sel teal

> color sel medium aquamarine

> color sel dark cyan

> color sel cornflower blue

> color sel light sea green

> color sel medium turquoise

> color sel turquoise

> color sel dodger blue

> color sel medium spring green

> color sel dark turquoise

> color (#!1 & sel) #fbfff6ff

[Repeated 1 time(s)]

> color (#!1 & sel) #fefeffff

> color (#!1 & sel) #f7f1ffff

> color (#!1 & sel) #f6eeffff

> color (#!1 & sel) #f5edffff

> color (#!1 & sel) #f3e9ffff

> color (#!1 & sel) #ebdeffff

> color (#!1 & sel) #e6d5ffff

> color (#!1 & sel) #e5d4ffff

> color (#!1 & sel) #ebdcffff

[Repeated 1 time(s)]

> color (#!1 & sel) #eadaffff

> color (#!1 & sel) #ead9ffff

> color (#!1 & sel) #e9d8ffff

> color (#!1 & sel) #e8d5ffff

> color (#!1 & sel) #e5d1ffff

> color (#!1 & sel) #e2ccffff

> color (#!1 & sel) #e1c8ffff

> color (#!1 & sel) #dfc7ffff

> color (#!1 & sel) #dfc5ffff

> color (#!1 & sel) #dcc3ffff

> color (#!1 & sel) #d9bfffff

> color (#!1 & sel) #d1b2ffff

> color (#!1 & sel) #ceadffff

> color (#!1 & sel) #ceacffff

> color (#!1 & sel) #cdacffff

> color (#!1 & sel) #cba9ffff

> color (#!1 & sel) #c9a9ffff

> color (#!1 & sel) #c7a7ffff

> color (#!1 & sel) #c0a3ffff

> color (#!1 & sel) #bea2ffff

> color (#!1 & sel) #b9a1ffff

> color (#!1 & sel) #b7a0ffff

> color (#!1 & sel) #b19fffff

> color (#!1 & sel) #a99cffff

> color (#!1 & sel) #a59bffff

> color (#!1 & sel) #a49bffff

> color (#!1 & sel) #a29affff

> color (#!1 & sel) #9d98ffff

> color (#!1 & sel) #9c98ffff

> color (#!1 & sel) #9b98ffff

> color (#!1 & sel) #9a98ffff

> color (#!1 & sel) #9998ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #9999ffff

> color (#!1 & sel) #999bffff

> color (#!1 & sel) #9a9effff

> color (#!1 & sel) #9ba1ffff

> color (#!1 & sel) #9ba3ffff

> color (#!1 & sel) #94b3ffff

> color (#!1 & sel) #94b4ffff

> color (#!1 & sel) #92b7ffff

> color (#!1 & sel) #91b8ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #92b8ffff

> color (#!1 & sel) #93b7ffff

> color (#!1 & sel) #95b0ffff

> color (#!1 & sel) #96a9ffff

> color (#!1 & sel) #96a7ffff

> color (#!1 & sel) #96a5ffff

> color (#!1 & sel) #96a3ffff

> color (#!1 & sel) #95a1ffff

> color (#!1 & sel) #959effff

> color (#!1 & sel) #959bffff

> color (#!1 & sel) #9499ffff

> color (#!1 & sel) #9497ffff

> color (#!1 & sel) #9593ffff

> color (#!1 & sel) #9a92ffff

> color (#!1 & sel) #9c91ffff

> color (#!1 & sel) #9d90ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #9f8fffff

> color (#!1 & sel) #a08dffff

> color (#!1 & sel) #a18bffff

> color (#!1 & sel) #a28affff

> color (#!1 & sel) #a388ffff

> color (#!1 & sel) #a483ffff

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #c783ffff

> color (#!1 & sel) #cc83ffff

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #eb8dffff

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> color (#!1 & sel) #f092ffff

> color (#!1 & sel) #f192ffff

> color (#!1 & sel) #f495ffff

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #b2b2ffff

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[Repeated 1 time(s)]

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[Repeated 2 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #b6b7ffff

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> color (#!1 & sel) #b3b3ffff

> color (#!1 & sel) #b3b2ffff

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #aaa5ffff

> color (#!1 & sel) #a9a5ffff

> color (#!1 & sel) #a8a4ffff

> color (#!1 & sel) #a7a4ffff

> color (#!1 & sel) #a6a4ffff

> color (#!1 & sel) #a6a3ffff

> color (#!1 & sel) #a5a3ffff

> color (#!1 & sel) #a4a3ffff

[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #a89cffff

> color (#!1 & sel) #a79cffff

> color (#!1 & sel) #a79bffff

> color (#!1 & sel) #a79affff

> color (#!1 & sel) #a69affff

> color (#!1 & sel) #a699ffff

> color (#!1 & sel) #a698ffff

> color (#!1 & sel) #a597ffff

> color (#!1 & sel) #a495ffff

> color (#!1 & sel) #a494ffff

> color (#!1 & sel) #a393ffff

> color (#!1 & sel) #a392ffff

> color (#!1 & sel) #a291ffff

> color (#!1 & sel) #a290ffff

> color (#!1 & sel) #a18fffff

> color (#!1 & sel) #9f8fffff

> color (#!1 & sel) #9e8effff

> color (#!1 & sel) #9d8effff

> color (#!1 & sel) #9a8dffff

> color (#!1 & sel) #978dffff

> color (#!1 & sel) #968cffff

> color (#!1 & sel) #948cffff

> color (#!1 & sel) #938bffff

> color (#!1 & sel) #928bffff

> color (#!1 & sel) #918bffff

> color (#!1 & sel) #8f8affff

> color (#!1 & sel) #8e8affff

> color (#!1 & sel) #8d89ffff

> color (#!1 & sel) #8b89ffff

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> color (#!1 & sel) #8787ffff

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #788fffff

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> color (#!1 & sel) #7490ffff

[Repeated 1 time(s)]

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[Repeated 2 time(s)]

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> color (#!1 & sel) #768fffff

> color (#!1 & sel) #798dffff

> color (#!1 & sel) #7a89ffff

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> color (#!1 & sel) #7a7dffff

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> color (#!1 & sel) #8078ffff

> color (#!1 & sel) #8377ffff

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> color (#!1 & sel) #8a72ffff

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> color (#!1 & sel) #9065ffff

[Repeated 1 time(s)]

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> color (#!1 & sel) #9767ffff

> color (#!1 & sel) #9867ffff

> color (#!1 & sel) #9967ffff

> color (#!1 & sel) #9b67ffff

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[Repeated 1 time(s)]

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> color (#!1 & sel) #9f68ffff

> color (#!1 & sel) #a168ffff

> color (#!1 & sel) #a268ffff

> color (#!1 & sel) #a269ffff

> color (#!1 & sel) #a56dffff

> color (#!1 & sel) #a975ffff

> color (#!1 & sel) #ac7cffff

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> color (#!1 & sel) #ae81ffff

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> color (#!1 & sel) #b086ffff

> color (#!1 & sel) #b189ffff

> color (#!1 & sel) #b28effff

> color (#!1 & sel) #b392ffff

> color (#!1 & sel) #b495ffff

> color (#!1 & sel) #b397ffff

> color (#!1 & sel) #b398ffff

> color (#!1 & sel) #b298ffff

> color (#!1 & sel) #b098ffff

> color (#!1 & sel) #ae97ffff

> color (#!1 & sel) #ac97ffff

> color (#!1 & sel) #a996ffff

> color (#!1 & sel) #a795ffff

> color (#!1 & sel) #a294ffff

> color (#!1 & sel) #9f93ffff

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> color (#!1 & sel) #9a91ffff

> color (#!1 & sel) #9790ffff

> color (#!1 & sel) #958fffff

> color (#!1 & sel) #938fffff

[Repeated 1 time(s)]

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> color (#!1 & sel) #9790ffff

> color (#!1 & sel) #9890ffff

> color (#!1 & sel) #9991ffff

> color (#!1 & sel) #9a91ffff

> color (#!1 & sel) #9b92ffff

> color (#!1 & sel) #9d92ffff

[Repeated 1 time(s)]

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> color (#!1 & sel) #9991ffff

> color (#!1 & sel) #9890ffff

> color (#!1 & sel) #9790ffff

> color (#!1 & sel) #9690ffff

> color (#!1 & sel) #938fffff

> color (#!1 & sel) #8c8dffff

> color (#!1 & sel) #8c8effff

> color (#!1 & sel) #8b8effff

> color (#!1 & sel) #8b8fffff

> color (#!1 & sel) #8a8fffff

> color (#!1 & sel) #8691ffff

> color (#!1 & sel) #8492ffff

> color (#!1 & sel) #8392ffff

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> color (#!1 & sel) #8094ffff

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> color (#!1 & sel) #7c94ffff

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> color (#!1 & sel) #7297ffff

> color (#!1 & sel) #7197ffff

> color (#!1 & sel) #7097ffff

> color (#!1 & sel) #6e98ffff

> color (#!1 & sel) #6c99ffff

> color (#!1 & sel) #6b9affff

> color (#!1 & sel) #6a9bffff

[Repeated 1 time(s)]

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> color (#!1 & sel) #699effff

> color (#!1 & sel) #68a0ffff

> color (#!1 & sel) #68a1ffff

> color (#!1 & sel) #69a3ffff

> color (#!1 & sel) #69a7ffff

> color (#!1 & sel) #69a8ffff

> color (#!1 & sel) #6aa9ffff

> color (#!1 & sel) #6bacffff

> color (#!1 & sel) #6baeffff

> color (#!1 & sel) #6cafffff

> color (#!1 & sel) #6cb0ffff

> color (#!1 & sel) #6db2ffff

> color (#!1 & sel) #6fb3ffff

> color (#!1 & sel) #70b4ffff

> color (#!1 & sel) #73b6ffff

> color (#!1 & sel) #76b8ffff

> color (#!1 & sel) #82beffff

> color (#!1 & sel) #8ac1ffff

> color (#!1 & sel) #8dc3ffff

> color (#!1 & sel) #8ec3ffff

> color (#!1 & sel) #90c4ffff

> color (#!1 & sel) #93c5ffff

> color (#!1 & sel) #9bc9ffff

> color (#!1 & sel) #9ccaffff

> color (#!1 & sel) #9dcaffff

> color (#!1 & sel) #a0caffff

> color (#!1 & sel) #a4cbffff

> color (#!1 & sel) #a5cbffff

> color (#!1 & sel) #a5caffff

> color (#!1 & sel) #a5c9ffff

> color (#!1 & sel) #a6c6ffff

> color (#!1 & sel) #a5c4ffff

> color (#!1 & sel) #a4beffff

> color (#!1 & sel) #a3baffff

> color (#!1 & sel) #a2b7ffff

> color (#!1 & sel) #a0b3ffff

> color (#!1 & sel) #9cacffff

> color (#!1 & sel) #9baaffff

> color (#!1 & sel) #99a7ffff

> color (#!1 & sel) #99a6ffff

> color (#!1 & sel) #97a4ffff

> color (#!1 & sel) #97a3ffff

> color (#!1 & sel) #95a1ffff

> color (#!1 & sel) #939dffff

> color (#!1 & sel) #939cffff

> color (#!1 & sel) #929bffff

> color (#!1 & sel) #919affff

> color (#!1 & sel) #8e96ffff

> color (#!1 & sel) #8c93ffff

> color (#!1 & sel) #8c92ffff

> color (#!1 & sel) #8a90ffff

> color (#!1 & sel) #8a8fffff

> color (#!1 & sel) #898effff

> color (#!1 & sel) #888dffff

> color (#!1 & sel) #888cffff

> color (#!1 & sel) #878bffff

> color (#!1 & sel) #8689ffff

> color (#!1 & sel) #8486ffff

> color (#!1 & sel) #8485ffff

> color (#!1 & sel) #8484ffff

> color (#!1 & sel) #8383ffff

> color (#!1 & sel) #8483ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #8482ffff

> color (#!1 & sel) #8582ffff

> color (#!1 & sel) #8782ffff

> color (#!1 & sel) #8781ffff

> color (#!1 & sel) #8881ffff

> color (#!1 & sel) #8981ffff

> color (#!1 & sel) #8c80ffff

> color (#!1 & sel) #8d80ffff

> color (#!1 & sel) #8e80ffff

[Repeated 2 time(s)]

> color (#!1 & sel) #8f80ffff

> color (#!1 & sel) #9180ffff

> color (#!1 & sel) #9281ffff

> color (#!1 & sel) #9482ffff

> color (#!1 & sel) #9682ffff

> color (#!1 & sel) #9883ffff

> color (#!1 & sel) #9983ffff

> color (#!1 & sel) #9a83ffff

> color (#!1 & sel) #9b84ffff

> color (#!1 & sel) #9c84ffff

> color (#!1 & sel) #9d84ffff

> color (#!1 & sel) #9e84ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #8484ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #8478ffff

> color (#!1 & sel) #8478adff

> select clear

> select #1/H-N:16-35

1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected  

> color (#!1 & sel) #a878adff

> color (#!1 & sel) #a897adff

> color (#!1 & sel) #a897dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897dbff

> color (#!1 & sel) #a897daff

> color (#!1 & sel) #a897d8ff

> color (#!1 & sel) #a897d5ff

> color (#!1 & sel) #a897d4ff

> color (#!1 & sel) #a897d2ff

> color (#!1 & sel) #a897d0ff

> color (#!1 & sel) #a897ceff

> color (#!1 & sel) #a897cdff

> color (#!1 & sel) #a897cbff

> color (#!1 & sel) #a897c6ff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897c5ff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897c3ff

> color (#!1 & sel) #a897c0ff

> color (#!1 & sel) #a897bfff

> color (#!1 & sel) #a897beff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897bcff

> color (#!1 & sel) #a897bbff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897beff

> color (#!1 & sel) #a897bfff

> color (#!1 & sel) #a897c1ff

> color (#!1 & sel) #a897c3ff

> color (#!1 & sel) #a897c7ff

> color (#!1 & sel) #a897c8ff

> color (#!1 & sel) #a897caff

> color (#!1 & sel) #a897ceff

> color (#!1 & sel) #a897d2ff

> color (#!1 & sel) #a897d4ff

> color (#!1 & sel) #a897d5ff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897d6ff

> color (#!1 & sel) #a897d7ff

> color (#!1 & sel) #a897d8ff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897d9ff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897daff

> color (#!1 & sel) #a897dbff

> color (#!1 & sel) #a897dcff

[Repeated 2 time(s)]

> color (#!1 & sel) #a89bdcff

> color (#!1 & sel) #a89edcff

> color (#!1 & sel) #a89fdcff

> color (#!1 & sel) #a8a0dcff

> color (#!1 & sel) #a8a1dcff

[Repeated 2 time(s)]

> color (#!1 & sel) #a8a0dcff

> color (#!1 & sel) #a89edcff

> color (#!1 & sel) #a89ddcff

> color (#!1 & sel) #a89cdcff

> color (#!1 & sel) #a89adcff

> color (#!1 & sel) #a898dcff

> color (#!1 & sel) #a895dcff

> color (#!1 & sel) #a891dcff

> color (#!1 & sel) #a88fdcff

> color (#!1 & sel) #a88bdcff

> color (#!1 & sel) #a88adcff

> color (#!1 & sel) #a887dcff

> color (#!1 & sel) #a886dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a887dcff

> color (#!1 & sel) #a888dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a88adcff

> color (#!1 & sel) #a88bdcff

> color (#!1 & sel) #a88cdcff

> color (#!1 & sel) #a88edcff

> color (#!1 & sel) #a88fdcff

> color (#!1 & sel) #a891dcff

> color (#!1 & sel) #a894dcff

> color (#!1 & sel) #a895dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a896dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a897dcff

[Repeated 2 time(s)]

> color (#!1 & sel) #a697dcff

> color (#!1 & sel) #a597dcff

> color (#!1 & sel) #a397dcff

> color (#!1 & sel) #a197dcff

> color (#!1 & sel) #9f97dcff

> color (#!1 & sel) #9d97dcff

> color (#!1 & sel) #9c97dcff

[Repeated 4 time(s)]

> color (#!1 & sel) #9d97dcff

> color (#!1 & sel) #9e97dcff

> color (#!1 & sel) #9f97dcff

[Repeated 2 time(s)]

> color (#!1 & sel) #9e97dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e96dcff

> color (#!1 & sel) #9e94dcff

> color (#!1 & sel) #9e93dcff

> color (#!1 & sel) #9e92dcff

> color (#!1 & sel) #9e91dcff

> color (#!1 & sel) #9e8fdcff

> color (#!1 & sel) #9e8edcff

> color (#!1 & sel) #9e8ddcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e8edcff

> color (#!1 & sel) #9e8fdcff

> color (#!1 & sel) #9e90dcff

> color (#!1 & sel) #9e91dcff

> color (#!1 & sel) #9e92dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e93dcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e92dcff

> color (#!1 & sel) #9e91dcff

> color (#!1 & sel) #9e90dcff

> color (#!1 & sel) #9e8fdcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e8edcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e8ddcff

[Repeated 2 time(s)]

> color (#!1 & sel) #9e8dd9ff

> color (#!1 & sel) #9e8dd8ff

> color (#!1 & sel) #9e8dd6ff

> color (#!1 & sel) #9e8dd3ff

> color (#!1 & sel) #9e8dd2ff

> color (#!1 & sel) #9e8dcfff

> color (#!1 & sel) #9e8dccff

> color (#!1 & sel) #9e8dc9ff

> color (#!1 & sel) #9e8dc5ff

> color (#!1 & sel) #9e8dc1ff

> color (#!1 & sel) #9e8dbfff

> color (#!1 & sel) #9e8dbeff

> color (#!1 & sel) #9e8dbdff

> color (#!1 & sel) #9e8dbbff

> color (#!1 & sel) #9e8db9ff

> color (#!1 & sel) #9e8db8ff

> color (#!1 & sel) #9e8db7ff

> color (#!1 & sel) #9e8db6ff

> color (#!1 & sel) #9e8db1ff

> color (#!1 & sel) #9e8daaff

> color (#!1 & sel) #9e8da2ff

> color (#!1 & sel) #9e8d98ff

> color (#!1 & sel) #9e8d90ff

> color (#!1 & sel) #9e8d89ff

> color (#!1 & sel) #9e8d85ff

> color (#!1 & sel) #9e8d83ff

> color (#!1 & sel) #9e8d81ff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e8d80ff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e8d8aff

> color (#!1 & sel) #9e8d8fff

> color (#!1 & sel) #9e8d97ff

> color (#!1 & sel) #9e8d9fff

> color (#!1 & sel) #9e8da6ff

> color (#!1 & sel) #9e8dadff

> color (#!1 & sel) #9e8db2ff

> color (#!1 & sel) #9e8db6ff

> color (#!1 & sel) #9e8dbaff

> color (#!1 & sel) #9e8dbeff

> color (#!1 & sel) #9e8dc0ff

> color (#!1 & sel) #9e8dc2ff

> color (#!1 & sel) #9e8dc4ff

> color (#!1 & sel) #9e8dc6ff

> color (#!1 & sel) #9e8dc7ff

> color (#!1 & sel) #9e8dc6ff

> color (#!1 & sel) #9e8dc4ff

> color (#!1 & sel) #9e8dc2ff

> color (#!1 & sel) #9e8dc1ff

> color (#!1 & sel) #9e8dc0ff

> color (#!1 & sel) #9e8dbfff

[Repeated 2 time(s)]

> color (#!1 & sel) #9e8dbeff

> color (#!1 & sel) #9e8dbdff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e8dbcff

[Repeated 2 time(s)]

> color (#!1 & sel) #9e8fbcff

> color (#!1 & sel) #9e91bcff

> color (#!1 & sel) #9e93bcff

> color (#!1 & sel) #9e96bcff

> color (#!1 & sel) #9e99bcff

> color (#!1 & sel) #9e9abcff

> color (#!1 & sel) #9e9bbcff

> color (#!1 & sel) #9e9cbcff

> color (#!1 & sel) #9e9ebcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e9dbcff

> color (#!1 & sel) #9e99bcff

> color (#!1 & sel) #9e97bcff

> color (#!1 & sel) #9e95bcff

> color (#!1 & sel) #9e93bcff

> color (#!1 & sel) #9e91bcff

> color (#!1 & sel) #9e8ebcff

> color (#!1 & sel) #9e8cbcff

> color (#!1 & sel) #9e8abcff

> color (#!1 & sel) #9e88bcff

> color (#!1 & sel) #9e86bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e85bcff

[Repeated 2 time(s)]

> color (#!1 & sel) #9e86bcff

> color (#!1 & sel) #9e88bcff

> color (#!1 & sel) #9e89bcff

> color (#!1 & sel) #9e8bbcff

> color (#!1 & sel) #9e8cbcff

> color (#!1 & sel) #9e8dbcff

> color (#!1 & sel) #9e8ebcff

> color (#!1 & sel) #9e8fbcff

> color (#!1 & sel) #9e90bcff

> color (#!1 & sel) #9e91bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e92bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9f92bcff

> color (#!1 & sel) #a192bcff

> color (#!1 & sel) #a392bcff

> color (#!1 & sel) #a592bcff

> color (#!1 & sel) #a692bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a892bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a992bcff

> color (#!1 & sel) #aa92bcff

> color (#!1 & sel) #a992bcff

> color (#!1 & sel) #a892bcff

> color (#!1 & sel) #a692bcff

> color (#!1 & sel) #a592bcff

> color (#!1 & sel) #a492bcff

> color (#!1 & sel) #a392bcff

> color (#!1 & sel) #a292bcff

> color (#!1 & sel) #a192bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a092bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9f92bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9e92bcff

[Repeated 2 time(s)]

> color (#!1 & sel) #9f92bcff

[Repeated 2 time(s)]

> color (#!1 & sel) #a092bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a192bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #a292bcff

[Repeated 3 time(s)]

> color (#!1 & sel) #a092bcff

> color (#!1 & sel) #9f92bcff

> color (#!1 & sel) #9e92bcff

> color (#!1 & sel) #9d92bcff

[Repeated 2 time(s)]

> color (#!1 & sel) #9d91bcff

> color (#!1 & sel) #9d90bcff

> color (#!1 & sel) #9d8fbcff

> color (#!1 & sel) #9d8ebcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d8dbcff

> color (#!1 & sel) #9d8cbcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d8dbcff

> color (#!1 & sel) #9d8ebcff

> color (#!1 & sel) #9d8fbcff

> color (#!1 & sel) #9d90bcff

> color (#!1 & sel) #9d91bcff

> color (#!1 & sel) #9d92bcff

[Repeated 3 time(s)]

> color (#!1 & sel) #9d93bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d92bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d91bcff

> color (#!1 & sel) #9d90bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d91bcff

[Repeated 2 time(s)]

> color (#!1 & sel) #9d92bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d93bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d93bbff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d93baff

> color (#!1 & sel) #9d93b9ff

> color (#!1 & sel) #9d93b8ff

> color (#!1 & sel) #9d93b7ff

[Repeated 2 time(s)]

> color (#!1 & sel) #9d93b6ff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d93b7ff

> color (#!1 & sel) #9d93b8ff

> color (#!1 & sel) #9d93b9ff

> color (#!1 & sel) #9d93baff

> color (#!1 & sel) #9d93bbff

> color (#!1 & sel) #9d93bcff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d93bdff

[Repeated 1 time(s)]

> color (#!1 & sel) #9d93beff

> color (#!1 & sel) #9d93bfff

[Repeated 1 time(s)]

> select clear

> select #1/H-N:16-35

1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected  

> color (#!1 & sel) #9d93bfff

> color (#!1 & sel) #2093bfff

[Repeated 1 time(s)]

> color (#!1 & sel) #201ebfff

> color (#!1 & sel) #201e2aff

> color (#!1 & sel) #771e2aff

> color (#!1 & sel) #776d2aff

> color (#!1 & sel) #776d9cff

[Repeated 1 time(s)]

> color (#!1 & sel) #776d98ff

[Repeated 1 time(s)]

> color (#!1 & sel) #776d97ff

> color (#!1 & sel) #776d96ff

> color (#!1 & sel) #776d95ff

> color (#!1 & sel) #776d94ff

> color (#!1 & sel) #776d93ff

> color (#!1 & sel) #776d92ff

> color (#!1 & sel) #776d91ff

[Repeated 1 time(s)]

> color (#!1 & sel) #776d90ff

[Repeated 1 time(s)]

> color (#!1 & sel) #776d8fff

[Repeated 1 time(s)]

> color (#!1 & sel) #776e8fff

[Repeated 1 time(s)]

> color (#!1 & sel) #77708fff

> color (#!1 & sel) #77728fff

[Repeated 1 time(s)]

> color (#!1 & sel) #77748fff

[Repeated 1 time(s)]

> color (#!1 & sel) #77738fff

[Repeated 1 time(s)]

> color (#!1 & sel) #77728fff

> color (#!1 & sel) #77718fff

> color (#!1 & sel) #77708fff

[Repeated 2 time(s)]

> color (#!1 & sel) #78708fff

> color (#!1 & sel) #7a708fff

[Repeated 1 time(s)]

> color (#!1 & sel) #7b708fff

> color (#!1 & sel) #7a708fff

[Repeated 1 time(s)]

> color (#!1 & sel) #79708fff

[Repeated 1 time(s)]

> color (#!1 & sel) #78708fff

[Repeated 2 time(s)]

> color (#!1 & sel) #77708fff

[Repeated 1 time(s)]

> color (#!1 & sel) #777090ff

> color (#!1 & sel) #777092ff

> color (#!1 & sel) #777093ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777094ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777095ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777096ff

[Repeated 2 time(s)]

> color (#!1 & sel) #777097ff

> color (#!1 & sel) #777098ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777099ff

[Repeated 3 time(s)]

> color (#!1 & sel) #777097ff

[Repeated 2 time(s)]

> color (#!1 & sel) #777096ff

> color (#!1 & sel) #777095ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777094ff

> color (#!1 & sel) #777093ff

[Repeated 2 time(s)]

> color (#!1 & sel) #777092ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777091ff

> color (#!1 & sel) #777090ff

[Repeated 2 time(s)]

> color (#!1 & sel) #777091ff

> color (#!1 & sel) #777092ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777093ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777094ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777095ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777295ff

> color (#!1 & sel) #777395ff

> color (#!1 & sel) #777495ff

> color (#!1 & sel) #777595ff

[Repeated 2 time(s)]

> color (#!1 & sel) #777495ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777395ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777295ff

> color (#!1 & sel) #777195ff

[Repeated 1 time(s)]

> color (#!1 & sel) #777295ff

[Repeated 2 time(s)]

> color (#!1 & sel) #787295ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7295ff

> color (#!1 & sel) #7b7295ff

> color (#!1 & sel) #7c7295ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7d7295ff

[Repeated 2 time(s)]

> color (#!1 & sel) #7c7295ff

> color (#!1 & sel) #7b7295ff

> color (#!1 & sel) #7a7295ff

[Repeated 3 time(s)]

> select clear

> select #1/H-N:16-35

1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected  

> color (#!1 & sel) #7a7295ff

> color (#!1 & sel) #7a7294ff

> color (#!1 & sel) #7a7293ff

> color (#!1 & sel) #7a7292ff

> color (#!1 & sel) #7a7291ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a728fff

> color (#!1 & sel) #7a728eff

> color (#!1 & sel) #7a728dff

> color (#!1 & sel) #7a728bff

> color (#!1 & sel) #7a728aff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7289ff

[Repeated 2 time(s)]

> color (#!1 & sel) #7a728aff

> color (#!1 & sel) #7a728cff

> color (#!1 & sel) #7a728dff

> color (#!1 & sel) #7a728fff

> color (#!1 & sel) #7a7290ff

> color (#!1 & sel) #7a7292ff

> color (#!1 & sel) #7a7293ff

> color (#!1 & sel) #7a7294ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7295ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7296ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7299ff

> color (#!1 & sel) #7a729bff

[Repeated 2 time(s)]

> color (#!1 & sel) #7a729aff

> color (#!1 & sel) #7a7299ff

> color (#!1 & sel) #7a7298ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7297ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7296ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7295ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7296ff

> color (#!1 & sel) #7a7297ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7298ff

[Repeated 2 time(s)]

> color (#!1 & sel) #7a7297ff

> color (#!1 & sel) #7a7296ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7295ff

> color (#!1 & sel) #7a7294ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7295ff

> color (#!1 & sel) #7a7296ff

[Repeated 1 time(s)]

> color (#!1 & sel) #7a7297ff

[Repeated 2 time(s)]

> select clear

> select ::name=""KHS""

2380 atoms, 2436 bonds, 56 residues, 4 models selected  

> style sel & #!1 sphere

Changed 658 atom styles  

> style sel & #!1 ball

Changed 658 atom styles  

> style sel & #!1 sphere

Changed 658 atom styles  

> style sel & #!1 stick

Changed 658 atom styles  

> style sel & #!1 sphere

Changed 658 atom styles  

> color (#!1 & sel) forest green

> color (#!1 & sel) lime

> color (#!1 & sel) light sea green

> color (#!1 & sel) forest green

> select clear

> save new_data_1.png width 2000 supersample 4

> graphics silhouettes true

> save new_data_1.png width 2000 supersample 4

> show #!3 models

> hide #!3 models

> save new_data_2.png width 2000 supersample 4

> save new_data_3.png width 2000 supersample 4

> show #!3 models

> ui tool show Matchmaker

> matchmaker #4#!2-3,5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1yg6, chain I
(#4), sequence alignment score = 934.6  
RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs:
2.818)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J
(#3), sequence alignment score = 937.6  
RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs:
2.425)  
  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 3mt6, chain E
(#5), sequence alignment score = 954.4  
RMSD between 181 pruned atom pairs is 0.466 angstroms; (across all 186 pairs:
0.661)  
  

> hide #!3 models

> show #4 models

> hide #!1 models

> select add #4

21540 atoms, 20901 bonds, 3585 residues, 1 model selected  

> surface sel

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> select subtract #4

14 models selected  

> show #!4 models

> select #3/H,I,J,K,L,M,N

10653 atoms, 10192 bonds, 1903 residues, 1 model selected  

> color sel #7A7297

> select #4/H,I,J,K,L,M,N

10526 atoms, 10173 bonds, 1787 residues, 1 model selected  

> color sel #7A7297

> hide #!1 models

> show #!1 models

> color sel INDIGO

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel Indigo

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel indigo

> select #4/A-G

11014 atoms, 10728 bonds, 1798 residues, 1 model selected  

> color sel #7A7297

> select clear

> hide #!1 models

> save 1YG6_1.png width 2000 supersample 4

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> save 1YG6_1.png width 2000 supersample 4

> hide #!4 models

> show #!1 models

> save new_data_1.png width 2000 supersample 4

> show #!3 models

> hide #!1 models

> select #3/A-G

10655 atoms, 10192 bonds, 1905 residues, 1 model selected  

> color sel indigo

> select clear

> show #!1 models

> hide #!1 models

> select #3/A-G

10655 atoms, 10192 bonds, 1905 residues, 1 model selected  

> color sel #7A7297

> select #3/H-N

10653 atoms, 10192 bonds, 1903 residues, 1 model selected  

> color sel indigo

> select clear

> show #!1 models

> hide #!1 models

> save 1TYF_1.png width 2000 supersample 4

> show #!5 models

> hide #!3 models

> select clear

[Repeated 1 time(s)]

> select #5/Q:16

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

30 atoms, 30 bonds, 4 residues, 1 model selected  

> select up

1391 atoms, 1414 bonds, 179 residues, 1 model selected  

> select up

1407 atoms, 1429 bonds, 181 residues, 1 model selected  

> select up

1453 atoms, 1476 bonds, 187 residues, 1 model selected  

> select up

1594 atoms, 1490 bonds, 314 residues, 1 model selected  

> select up

46272 atoms, 43362 bonds, 9074 residues, 1 model selected  

> select down

1594 atoms, 1490 bonds, 314 residues, 1 model selected  

> select up

46272 atoms, 43362 bonds, 9074 residues, 1 model selected  

> select down

1594 atoms, 1490 bonds, 314 residues, 1 model selected  

> delete sel

[Repeated 1 time(s)]Drag select of 1000 residues, 6 pseudobonds  

> select clear

Drag select of 661 residues, 3 pseudobonds  

> select #5/R:130

4 atoms, 3 bonds, 1 residue, 1 model selected  
Drag select of 2287 residues, 6 pseudobonds  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/P:9

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select up

46 atoms, 45 bonds, 6 residues, 1 model selected  

> delete sel

> select clear

[Repeated 2 time(s)]

> select #5/X:12

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select up

15 atoms, 14 bonds, 3 residues, 1 model selected  

> delete sel

> select add #5

26835 atoms, 23694 bonds, 8 pseudobonds, 6464 residues, 2 models selected  

> show #!1 models

> hide #!1 models

> surface (#!5 & sel)

> select clear

> select #5/s:700@C1

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

26835 atoms, 23694 bonds, 6464 residues, 2 models selected  

> select clear

Drag select of 3mt6_Y SES surface, 3mt6_v SES surface, 1962 of 2742 triangles,
3mt6_y SES surface, 52 of 2758 triangles, 3mt6_z SES surface, 1186 of 2720
triangles, 2 residues  

> select clear

Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_v SES surface,
3mt6_w SES surface, 1558 of 2800 triangles, 3mt6_x SES surface, 186 of 2778
triangles, 3mt6_y SES surface, 2277 of 2758 triangles, 3mt6_z SES surface  
Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_Y SES surface,
3mt6_v SES surface, 3mt6_w SES surface, 3mt6_x SES surface, 3mt6_y SES
surface, 3mt6_z SES surface, 2 residues  

> select clear

Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_Y SES surface,
3mt6_v SES surface, 3mt6_w SES surface, 2690 of 2800 triangles, 3mt6_x SES
surface, 3mt6_y SES surface, 3mt6_z SES surface, 2143 of 2720 triangles, 2
residues  

> select clear

Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_O SES surface,
8882 of 178018 triangles, 3mt6_Y SES surface, 3mt6_v SES surface, 3mt6_w SES
surface, 3mt6_x SES surface, 3mt6_y SES surface, 3mt6_z SES surface, 2
residues  

> delete sel

> select #5/z:700@C6

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/3:700@C6

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/4:700@C6

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/v:700@C8

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/w:700@C7

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/y:700@C1

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/x:700@C2

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/s:700@C1

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/r:700@C6

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/q:700@C6

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/t:700@O11

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/u:700@O11

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/p:700@C1

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> select #5/O:12@NH1

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

46 atoms, 45 bonds, 6 residues, 2 models selected  

> select up

1474 atoms, 1497 bonds, 189 residues, 2 models selected  

> delete sel

> select #5/o:700@C2

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> delete sel

> show #!1 models

> hide #!1 models

> select #4/A-G

11014 atoms, 10728 bonds, 1798 residues, 1 model selected  

> select #5/A-G

11386 atoms, 10602 bonds, 4 pseudobonds, 2272 residues, 2 models selected  

> color sel indigo

> select #5/H-N

11312 atoms, 10523 bonds, 4 pseudobonds, 2271 residues, 2 models selected  

> color sel #7A7297

> select ::name=""GOL""

84 atoms, 70 bonds, 14 residues, 1 model selected  

> select ::name=""MP8""

112 atoms, 112 bonds, 14 residues, 1 model selected  

> select ::name=""MPD""

536 atoms, 469 bonds, 67 residues, 2 models selected  

> select ::name=""MP8""

112 atoms, 112 bonds, 14 residues, 1 model selected  

> select add ::name=""OTT""

238 atoms, 224 bonds, 28 residues, 15 models selected  

> select add ::name=""MAA""

322 atoms, 294 bonds, 42 residues, 15 models selected  

> select add ::name=""MPD""

858 atoms, 763 bonds, 109 residues, 16 models selected  

> select add ::name=""GOL""

942 atoms, 833 bonds, 123 residues, 17 models selected  

> select add ::name=""PRO""

7935 atoms, 7826 bonds, 828 residues, 22 models selected  

> select clear

> select #5/l:703@CG

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 7 bonds, 1 residue, 2 models selected  

> select up

52 atoms, 55 bonds, 7 residues, 2 models selected  

> select #5/A-N:703@CG

Nothing selected  

> select #5/A-N:703@CG

Nothing selected  

> select #5/A-N:703

Nothing selected  

> select #5/l:703@CG

1 atom, 1 residue, 1 model selected  

> select #5/a-n:703@CG

12 atoms, 12 residues, 1 model selected  

> select up

84 atoms, 84 bonds, 12 residues, 13 models selected  

> select up

624 atoms, 660 bonds, 84 residues, 13 models selected  

> color (#!5 & sel) red

> color sel crimson

> color sel fire brick

> color sel tomato

> color sel brown

> color sel tomato

> color sel indian red

> style sel sphere

Changed 624 atom styles  

> style sel sphere

Changed 624 atom styles  

> show sel atoms

> hide sel atoms

> select clear

> save 3MT6_1.png width 2000 supersample 4

> show #!2 models

> hide #!5 models

> select #2/A-G

10891 atoms, 10586 bonds, 6 pseudobonds, 1782 residues, 2 models selected  

> show #!1 models

> hide #!1 models

> color sel indigo

> select #2/H-N

10551 atoms, 10253 bonds, 6 pseudobonds, 1730 residues, 2 models selected  

> color sel #7A7297

> select clear

> select add #2

21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected  

> surface (#!2 & sel)

> select ::name=""KHS""

2380 atoms, 2436 bonds, 56 residues, 4 models selected  

> style sel & #!2 sphere

Changed 406 atom styles  

> color (#!2 & sel) forest green

> select clear

> show #!5 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> select #2/H-N

10551 atoms, 10253 bonds, 6 pseudobonds, 1730 residues, 2 models selected  

> color sel indigo

> select #2/A-G

10891 atoms, 10586 bonds, 6 pseudobonds, 1782 residues, 2 models selected  

> color sel #7A7297

> select clear

> select ::name=""KHS""

2380 atoms, 2436 bonds, 56 residues, 4 models selected  

> color (#!2 & sel) forest green

> select clear

> save 6NB1_1.png width 2000 supersample 4

> save ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Probac1_Figures/figures_prep.cxs"" includeMaps true

——— End of log from Thu Apr 9 16:14:06 2026 ———

opened ChimeraX session  

> hide #!2 models

> show #!1 models

> select #1/A-N:16-35

3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected  

> transparency (#!1 & sel) 80

> select #1/A-N:16-50

7280 atoms, 7308 bonds, 14 pseudobonds, 434 residues, 2 models selected  

> transparency (#!1 & sel) 80

> ui tool show ""Color Actions""

> color sel maroon

> select clear

> hide #1.1 models

> select #1/A-N:16-50

7280 atoms, 7308 bonds, 14 pseudobonds, 434 residues, 2 models selected  

> color sel brown

> select clear

> select #1/A-N:16-50

7280 atoms, 7308 bonds, 14 pseudobonds, 434 residues, 2 models selected  

> transparency (#!1 & sel) 90

> select clear

> cd ""/Users/ayomidefasemire/Documents/Doctoral/Main
> Project/ClpP/Probac1_Figures""

Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main
Project/ClpP/Probac1_Figures  

> save probac_loop.png width 2000 supersample 4

> show #!4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #4/A-N:1-50

5033 atoms, 5095 bonds, 616 residues, 1 model selected  

> select #4/A-N:1-35

3353 atoms, 3387 bonds, 406 residues, 1 model selected  

> transparency (#!4 & sel) 90

> color sel brown

> select clear

> select #4/A-N:1-35

3353 atoms, 3387 bonds, 406 residues, 1 model selected  

> transparency (#!4 & sel) 100

> select clear

> select #4/A-N:1-35

3353 atoms, 3387 bonds, 406 residues, 1 model selected  

> transparency (#!4 & sel) 95

> select clear

> save 1YG6_loop.png width 2000 supersample 4

> show #!1 models

> hide #!4 models

> save probac_loop2.png width 2000 supersample 4

> hide #!1 models

> show #!2 models

> select #2/A-N:1-35

1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected  

> transparency (#!2 & sel) 95

> hide #2.1 models

> select subtract #2.1

1241 atoms, 1253 bonds, 153 residues, 15 models selected  

> ui tool show ""Color Actions""

> color sel brown

> select clear

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> ui tool show ""Surface Color""

> select #2/A-N:1-35

1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected  

> color surface sel brown

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel surface brown

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color surface brown

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color surfaces brown

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color surfaces fromatoms

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color fromatoms surfaces

> transparency (#!2 & sel) 95

> transparency (#!2 & sel) 80

> select clear

> transparency (#!2 & sel) 90

> select #2/A-N:1-35

1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected  

> transparency (#!2 & sel) 80

> transparency (#!2 & sel) 95

> transparency (#!2 & sel) 80

> select clear

> transparency (#!2 & sel) 95

> select #2/A-N:1-35

1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected  

> transparency (#!2 & sel) 95

> select clear

> save 6NB1_loop.png width 2000 supersample 4

> hide #!2 models

> show #!5 models

> select #5/A-N:1-35

3712 atoms, 3746 bonds, 8 pseudobonds, 456 residues, 2 models selected  

> transparency (#!5 & sel) 95

> color sel brown

> select clear

> hide #4.1 models

> show #4.1 models

> hide #!4 models

> hide #5.1 models

> save 3MT6_loop.png width 2000 supersample 4

> hide #!5 models

> show #!1 models

> show #!2 models

> surface hidePatches #1.2-15#2.2-15#!1-2

> hide #!1 models

> show #!1 models

> select ::name=""KHS""

2380 atoms, 2436 bonds, 56 residues, 4 models selected  

> hide sel & #!1-2 atoms

> style sel & #!1-2 stick

Changed 1064 atom styles  

> hide sel & #!1-2 atoms

> show sel & #!1-2 atoms

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!2 models

> show #!2 models

> select #1 & KHS

Expected a keyword  

> select #1:KHS

658 atoms, 672 bonds, 14 residues, 1 model selected  

> color sel byhetero

> select clear

> select #2:KHS

406 atoms, 420 bonds, 14 residues, 1 model selected  

> color sel byhetero

> select clear

> select #2:KHS

406 atoms, 420 bonds, 14 residues, 1 model selected  

> color sel gold

> color sel goldenrod

> select clear

> select #2:KHS

406 atoms, 420 bonds, 14 residues, 1 model selected  

> color sel byhetero

> select clear

> select add #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> select add #2

63414 atoms, 63147 bonds, 26 pseudobonds, 6158 residues, 18 models selected  

> ui tool show ""Color Actions""

> color sel bychain

> hide #!2 models

> show #!2 models

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  

> matchmaker #2/A,B,C,D,E,F,G to #1/A,B,C,D,E,F,G alg bb pairing ss

Traceback (most recent call last):  
File
""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py"", line 319, in execute  
cmd.run(cmd_text)  
File
""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py"", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py"", line 767, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py"", line 269, in match  
raise ValueError(""Unknown sequence alignment algorithm: %s"" % alg)  
ValueError: Unknown sequence alignment algorithm: bb  
  
ValueError: Unknown sequence alignment algorithm: bb  
  
File
""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/match.py"", line 269, in match  
raise ValueError(""Unknown sequence alignment algorithm: %s"" % alg)  
  
See log for complete Python traceback.  
  

> matchmaker #2/A,B,C,D,E,F,G to #1/A,B,C,D,E,F,G

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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  

> ui tool show Matchmaker

> matchmaker #2/A#2/B#2/C#2/D#2/E#2/F#2/G to #1/A#1/B#1/C#1/D#1/E#1/F#1/G
> pairing ss

Parameters  
---  
Chain pairing | ss  
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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain B (#1) with 6nb1, chain B
(#2), sequence alignment score = 953.2  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain C (#1) with 6nb1, chain C
(#2), sequence alignment score = 925  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain D (#1) with 6nb1, chain D
(#2), sequence alignment score = 929.2  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain E (#1) with 6nb1, chain E
(#2), sequence alignment score = 928.6  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain F (#1) with 6nb1, chain F
(#2), sequence alignment score = 927.4  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain G (#1) with 6nb1, chain G
(#2), sequence alignment score = 932.8  
RMSD between 9 pruned atom pairs is 1.182 angstroms; (across all 1293 pairs:
30.045)  
  

> matchmaker #2/A#2/B#2/C#2/D#2/E#2/F#2/G#2/H#2/I#2/J#2/K#2/L#2/M#2/N to
> #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J#1/K#1/L#1/M#1/N pairing ss

Parameters  
---  
Chain pairing | ss  
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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain B (#1) with 6nb1, chain B
(#2), sequence alignment score = 953.2  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain C (#1) with 6nb1, chain C
(#2), sequence alignment score = 925  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain D (#1) with 6nb1, chain D
(#2), sequence alignment score = 929.2  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain E (#1) with 6nb1, chain E
(#2), sequence alignment score = 928.6  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain F (#1) with 6nb1, chain F
(#2), sequence alignment score = 927.4  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain G (#1) with 6nb1, chain G
(#2), sequence alignment score = 932.8  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain H (#1) with 6nb1, chain H
(#2), sequence alignment score = 931.6  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain I (#1) with 6nb1, chain I
(#2), sequence alignment score = 937.6  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain J (#1) with 6nb1, chain J
(#2), sequence alignment score = 933.4  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain K (#1) with 6nb1, chain K
(#2), sequence alignment score = 934.6  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain L (#1) with 6nb1, chain L
(#2), sequence alignment score = 935.8  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain M (#1) with 6nb1, chain M
(#2), sequence alignment score = 936.4  
Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain N (#1) with 6nb1, chain N
(#2), sequence alignment score = 936.4  
RMSD between 57 pruned atom pairs is 1.477 angstroms; (across all 2553 pairs:
47.524)  
  

> 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  

> 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A
(#2), sequence alignment score = 958.6  
RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs:
0.581)  
  

> select #2:KHS

406 atoms, 420 bonds, 14 residues, 1 model selected  

> color sel byelement

> color sel sandy brown

> color sel byelement

> color #1:KHS cornflower blue atoms

> select #2:KHS

406 atoms, 420 bonds, 14 residues, 1 model selected  

> select #1:KHS

658 atoms, 672 bonds, 14 residues, 1 model selected  

> color sel byelement

> color #1:KHS cornflower blue atoms

> color sel byhetero

> select clear

> hide #!2 models

> show #!2 models

> show #1/A,B cartoons

> hide #!1 models

> hide #!2 models

> show #1/A,B cartoons

> show #!1 models

> show #!2 models

> select #1/A,B

5996 atoms, 6044 bonds, 2 pseudobonds, 378 residues, 2 models selected  

> hide ~select cartoons

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide ~sel cartoons

> select ::name=""KHS""

2380 atoms, 2436 bonds, 56 residues, 4 models selected  

> select clear

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select #1-#2/A:KHS

Expected an objects specifier or a keyword  

> select #1-2/A:KHS

76 atoms, 78 bonds, 2 residues, 2 models selected  

> hide ~sel atoms

> select clear

> color #1:KHS cornflower blue atoms

> select #2/A:KHS coral atoms

Expected a keyword  

> color #2/A:KHS coral atoms

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> color sel magenta

> color sel dark violet

> color sel blue violet

> color sel dodger blue

> color sel dark cyan

> color sel teal

> color sel slate blue

> color sel dark turquoise

> color sel steel blue

> color sel dark cyan

> color sel medium aquamarine

> color sel cadet blue

> color sel steel blue

> color sel green

> color sel lime

> color sel olive

> select #2/A:KHS

29 atoms, 30 bonds, 1 residue, 1 model selected  

> color sel dark salmon

> color sel light salmon

> color sel sea green

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> surface sel

> surface hidePatches (#!1 & sel)

> select clear

> show #!9 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> hide #!2 models

> fitmap #1 inMap #9

Fit molecule 16Mar26_flip_KHS_QMR_refined.pdb (#1) to map
ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) using 41972 atoms  
average map value = 0.05287, steps = 148  
shifted from previous position = 1.69  
rotated from previous position = 17.7 degrees  
atoms outside contour = 17973, contour level = 0.041998  
  
Position of 16Mar26_flip_KHS_QMR_refined.pdb (#1) relative to
ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) coordinates:  
Matrix rotation and translation  
1.00000000 0.00001079 -0.00007158 0.01250729  
-0.00001078 0.99999999 0.00010843 -0.00778132  
0.00007158 -0.00010843 0.99999999 -0.00077511  
Axis -0.83170304 -0.54902092 -0.08274110  
Axis point 0.00000000 -11.78504258 102.47368213  
Rotation angle (degrees) 0.00746999  
Shift along axis -0.00606611  
  

> hide #!1 models

> show #!2 models

> fitmap #2 inMap #9

Fit molecule 6nb1 (#2) to map ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9)
using 21442 atoms  
average map value = 0.05636, steps = 148  
shifted from previous position = 2.24  
rotated from previous position = 18.1 degrees  
atoms outside contour = 7504, contour level = 0.041998  
  
Position of 6nb1 (#2) relative to ClpP_volume_map_1_95A_bfactor_77_flip.mrc
(#9) coordinates:  
Matrix rotation and translation  
0.07384522 0.30681292 0.94890079 45.01290705  
0.03233871 -0.95173497 0.30521265 140.06556919  
0.99674525 0.00814774 -0.08020301 -27.34946097  
Axis -0.72939678 -0.11747463 -0.67392881  
Axis point 0.00000000 63.01213740 -44.09357674  
Rotation angle (degrees) 168.25025544  
Shift along axis -30.85483139  
  

> show #!1 models

> select add #9

2 models selected  

> color #9.1 light gray

> transparency sel 50

> transparency sel 70

> select #9

2 models selected  

> select clear

> hide #!2 models

> color zone #9 near #1 distance 5.04

> transparency #1.2-16#9.1 50

> undo

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> color zone #9 near sel distance 4 color blue

Expected a keyword  

> ui tool show ""Color Zone""

> color zone #9 near #1 distance 5.04

> undo

> color zone #9 near sel distance 2 farColor blue

> color zone #9 near sel distance 4 farColor blue

> color zone #9 near sel distance 4 Color blue

Expected a keyword  

> color zone #9 near sel distance 4

> color zone #9 near sel distance 2

> color zone #9 near sel distance 2 blue

Expected a keyword  

> color zone #9 near sel distance 2

> transparency sel 0

> select add #9

47 atoms, 48 bonds, 1 residue, 4 models selected  

> transparency sel 0

> transparency sel 50

> select clear

> show #!2 models

> transparency sel 60

> select add #9

2 models selected  

> transparency sel 60

> transparency sel 40

> select #9

2 models selected  

> select #9

2 models selected  

> select #9

2 models selected  

> select subtract #9

Nothing selected  

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> save ACP_position.png width 2000 supersample 4

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) byhetero

> select #9

2 models selected  

> select #2/A:KHS

29 atoms, 30 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select add #2

21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected  

> select subtract #2

14 models selected  

> save ACP_position2.png width 2000 supersample 4

> graphics silhouettes false

> graphics silhouettes true

> lighting intensity 0.6

> lighting intensity 0.9

> lighting intensity 1.2

> lighting intensity 1.4

> save ACP_position3.png width 2000 supersample 4

> ui tool show ""Color Actions""

> hide #!9 models

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select add zone #1/A,B 4.0

Expected an objects specifier or a keyword  

> select sel @ select sel @ undo

> show sel atoms

> select add #3

21792 atoms, 20779 bonds, 3899 residues, 20 models selected  

> select subtract #3

484 atoms, 395 bonds, 91 residues, 31 models selected  

> select add #4

21978 atoms, 21260 bonds, 3662 residues, 17 models selected  

> select subtract #4

438 atoms, 359 bonds, 77 residues, 28 models selected  

> select add #5

25588 atoms, 22371 bonds, 8 pseudobonds, 6318 residues, 15 models selected  

> select subtract #5

369 atoms, 301 bonds, 59 residues, 38 models selected  

> select add #6

42216 atoms, 42500 bonds, 14 pseudobonds, 2690 residues, 11 models selected  

> select subtract #6

244 atoms, 192 bonds, 44 residues, 9 models selected  

> select add #7

5532 atoms, 5604 bonds, 704 residues, 9 models selected  

> select subtract #7

230 atoms, 188 bonds, 36 residues, 8 models selected  

> select add #10

42106 atoms, 42417 bonds, 14 pseudobonds, 2668 residues, 9 models selected  

> select subtract #10

134 atoms, 109 bonds, 22 residues, 7 models selected  

> undo

> hide sel & #!1-2 atoms

> undo

> show sel & #!1-2 cartoons

> undo

> select sel @ select clear

> hide #!1-2 atoms

> show #!1-2 atoms

> undo

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> select #2/A:KHS

29 atoms, 30 bonds, 1 residue, 1 model selected  

> hide ~sel atoms

> show #!1 models

> select #1-2/A:KHS

76 atoms, 78 bonds, 2 residues, 2 models selected  

> show sel atoms

> select sel : select add #2

23076 atoms, 22426 bonds, 12 pseudobonds, 3644 residues, 20 models selected  

> select subtract #2

1634 atoms, 1587 bonds, 132 residues, 30 models selected  

> select add #3

22802 atoms, 21841 bonds, 3919 residues, 16 models selected  

> select subtract #3

1494 atoms, 1457 bonds, 111 residues, 27 models selected  

> select add #4

22886 atoms, 22217 bonds, 3677 residues, 13 models selected  

> select subtract #4

1346 atoms, 1316 bonds, 92 residues, 24 models selected  

> select add #5

26394 atoms, 23218 bonds, 8 pseudobonds, 6329 residues, 11 models selected  

> select subtract #5

1175 atoms, 1148 bonds, 70 residues, 34 models selected  

> select add #6

42790 atoms, 43103 bonds, 14 pseudobonds, 2697 residues, 7 models selected  

> select subtract #6

818 atoms, 795 bonds, 51 residues, 5 models selected  

> select add #7

5993 atoms, 6090 bonds, 705 residues, 5 models selected  

> select subtract #7

691 atoms, 674 bonds, 37 residues, 4 models selected  

> select add #10

42294 atoms, 42621 bonds, 14 pseudobonds, 2664 residues, 5 models selected  

> select subtract #10

322 atoms, 313 bonds, 18 residues, 3 models selected  

> show sel atoms

> select clear

> style sel stick

Changed 322 atom styles  

> select clear

> undo

> hide sel atoms

> label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}""

> label (#!1 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label height 0.9

> label height 1.2

> undo

> hide sel atoms

> label offset 1,1,1

> label offset 1,2,1

> hide sel atoms

> label offset 1,0,1

> label offset 0,0,1

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!9 models

> label delete

> select clear

> save ACP_position4.png width 2000 supersample 4

> hide #!9 models

> hide #!2 models

> show #!2 models

> select #2/A:KHS

29 atoms, 30 bonds, 1 residue, 1 model selected  

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/A:KHS

29 atoms, 30 bonds, 1 residue, 1 model selected  

> select sel : show sel & #!1-2 atoms

> undo

> select add #3

22784 atoms, 21818 bonds, 3917 residues, 20 models selected  

> select subtract #3

1476 atoms, 1434 bonds, 109 residues, 31 models selected  

> select add #4

22904 atoms, 22231 bonds, 3679 residues, 17 models selected  

> select subtract #4

1364 atoms, 1330 bonds, 94 residues, 28 models selected  

> select add #5

26421 atoms, 23240 bonds, 8 pseudobonds, 6333 residues, 15 models selected  

> select subtract #5

1202 atoms, 1170 bonds, 74 residues, 38 models selected  

> select add #6

42861 atoms, 43171 bonds, 14 pseudobonds, 2704 residues, 11 models selected  

> select subtract #6

889 atoms, 863 bonds, 58 residues, 9 models selected  

> select add #7

6085 atoms, 6177 bonds, 715 residues, 9 models selected  

> select subtract #7

783 atoms, 761 bonds, 47 residues, 8 models selected  

> select add #10

42430 atoms, 42751 bonds, 14 pseudobonds, 2677 residues, 9 models selected  

> select subtract #10

458 atoms, 443 bonds, 31 residues, 7 models selected  

> show sel atoms

> select add #2

21767 atoms, 21157 bonds, 12 pseudobonds, 3528 residues, 8 models selected  

> select subtract #2

325 atoms, 318 bonds, 16 residues, 18 models selected  

> select add #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 5 models selected  

> select subtract #1

15 models selected  

> undo

> select add #2

21767 atoms, 21157 bonds, 12 pseudobonds, 3528 residues, 8 models selected  

> select subtract #2

325 atoms, 318 bonds, 16 residues, 18 models selected  

> show sel atoms

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> hide sel atoms

> undo

> label (#!1 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label height 1.2

> save ACP_pos_exp.png width 2000 supersample 4

> select clear

> save ACP_pos_exp.png width 2000 supersample 4

> label delete

> select add #1

41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected  

> select subtract #1

15 models selected  

> show #!1-2 atoms

> undo

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:KHS

29 atoms, 30 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select sel : label (#!1-2 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label height 1.2

> select clear

> save ACP_pos_exp2.png width 2000 supersample 4

> label delete

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> select add #2

21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected  

> select subtract #2

14 models selected  

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select sel : select add #3

22538 atoms, 21591 bonds, 3898 residues, 19 models selected  

> select subtract #3

1230 atoms, 1207 bonds, 90 residues, 30 models selected  

> select add #2

22569 atoms, 21944 bonds, 12 pseudobonds, 3594 residues, 17 models selected  

> select subtract #2

1127 atoms, 1105 bonds, 82 residues, 27 models selected  

> select add #4

22552 atoms, 21893 bonds, 3653 residues, 13 models selected  

> select subtract #4

1012 atoms, 992 bonds, 68 residues, 24 models selected  

> select add #5

26091 atoms, 22923 bonds, 8 pseudobonds, 6309 residues, 11 models selected  

> select subtract #5

872 atoms, 853 bonds, 50 residues, 34 models selected  

> select add #6

42561 atoms, 42880 bonds, 14 pseudobonds, 2681 residues, 7 models selected  

> select subtract #6

589 atoms, 572 bonds, 35 residues, 5 models selected  

> select add #7

5817 atoms, 5918 bonds, 695 residues, 5 models selected  

> select subtract #7

515 atoms, 502 bonds, 27 residues, 4 models selected  

> select add #10

42206 atoms, 42535 bonds, 14 pseudobonds, 2659 residues, 5 models selected  

> select subtract #10

234 atoms, 227 bonds, 13 residues, 3 models selected  

> select sticks

Expected an objects specifier or a keyword  

> style sel stick

Changed 234 atom styles  

> style sel stick

Changed 234 atom styles  

> show sel atoms

> select clear

> undo

> hide ~sel cartoons

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> lighting full

> lighting soft

> lighting simple

> clip off

> clip on

Expected a keyword  

> clip far

Missing ""far"" keyword's argument  

> clip #1 far

Expected a keyword  

> clip model #1 far

Expected true or false or a keyword  

> clip model #1 true

> hide ~sel cartoons

> label (#!1 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label delete

> select clear

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select sel : color (#!1-2 & sel) byhetero

> select clear

> undo

> select clear

> clip list

Clipping is off  

> clip near on

Invalid ""near"" argument: Expected 'off' or a number  

> clip far on #1

Invalid ""far"" argument: Expected 'off' or a number  

> clip model #1 true

> clip model #1 false

> clip front

Missing ""front"" keyword's argument  

> clip on

Expected a keyword  

> ui tool show ""Side View""

> hide H

> label #1.2-16#2.2-15#!1-2 text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label delete

> save ACP_compare1.png width 2000 supersample 4

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select sel : label (#!1-2 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> select clear

> save ACP_compare2.png width 2000 supersample 4

> label offset 1,1,1

> label offset 0.5,1,1

> label offset 0.5,0.5,1

> label offset 0.5,0.5,0.5

> label offset 0.5,0.5,1

> label offset 0.5,0.7,1

> label offset 0.5,0.5,1

> label offset 0.6,0.5,1

> label offset 0.5,0.5,1

> save ACP_compare2.png width 2000 supersample 4

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select sel : color (#!1-2 & sel) byhetero

> select clear

> save ACP_compare2.png width 2000 supersample 4

> label delete

> save ACP_compare1.png width 2000 supersample 4

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select sel : label (#!1-2 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label offset 0.5,0.5,1

> label offset 1,0.5,1

> label offset 0,0.5,1

> label offset 0.2,0.5,1

> label offset 0.2,0,1

> label offset 0.2,0.4,1

> label offset 0.4,0.4,1

> label offset 0.4,0.2,1

> label offset 0.5,0.2,1

> label offset 0.4,0.2,1

> select clear

> label offset 0.5,0.2,1

> label offset 0.3,0.2,1

> label offset 0.4,0.2,1

> label offset 0.4,0.4,1

> label offset 0.4,0.3,1

> label offset 0.5,0.3,1

> select clear

> label offset 0.6,0.3,1

> save ACP_compare2.png width 2000 supersample 4

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> select sel : select clear

> label delete

> save ACP_compare1.png width 2000 supersample 4

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> hbonds sel restrict both reveal true color yellow linewidth 3 log true
> dashes 8 dashesScale 0.5 label true labelColor white labelSize 1.2

Expected a keyword  

> ui tool show H-Bonds

> hbonds sel color #fad439 dashes 4 showDist true restrict both interModel
> false intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict both interModel
> false saltOnly true intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true interModel false intraMol
> false intraRes false reveal true

0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop
> 0.5 intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds sel restrict both reveal true color yellow linewidth 3 log true
> dashes 8 dashesScale 0.5 label true labelColor white labelSize 1.2

Expected a keyword  

> hbonds sel restrict both reveal true color yellow dashes 8

0 hydrogen bonds found  

> hbonds #1 & sel restrict both color yellow dashes 8

0 hydrogen bonds found  

> hbonds #1 & sel restrict both reveal true color yellow dashes 8 interModel
> false distSlop 0.4 angleSlop 30

0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop
> 0.5 intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop
> 0.5 intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop
> 0.5 intraMol false intraRes false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.5 angstroms and 20 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true intraModel false distSlop
> 0.5 intraMol false intraRes false reveal true log true
    
    
    Finding intermodel H-bonds
    Constraints relaxed by 0.5 angstroms and 20 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    	2 6nb1
    	3 1tyf
    	4 1yg6
    	5 3mt6
    	7 clpP_DHFR_PRBC_frank.pdb
    	6 28Mar_Final_shift_asym.pdb
    	10 28Mar_flip_KHS_QMR_refined.pdb
    
    4 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 NAS  3mt6 #5/E ILE 188 O                                16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 H9  1.920  1.022
    1tyf #3/J HOH 249 O                                16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  no hydrogen                                       3.078  N/A
    1tyf #3/J HOH 249 O                                16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAR  no hydrogen                                       2.811  N/A
    1tyf #3/J HOH 266 O                                16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  no hydrogen                                       3.205  N/A
    

  
4 hydrogen bonds found  

> select add #8.1

47 atoms, 48 bonds, 1 residue, 3 models selected  

> select subtract #8.1

47 atoms, 48 bonds, 1 residue, 2 models selected  

> close #8

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false intraModel false distSlop 0.5 intraMol false intraRes false reveal
> true log true
    
    
    Constraints relaxed by 0.5 angstroms and 20 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false intraModel false distSlop 0.5 saltOnly true intraMol false intraRes
> false reveal true log true
    
    
    Constraints relaxed by 0.5 angstroms and 20 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false distSlop 0.5 intraMol false intraRes false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.5 angstroms and 20 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false intraModel false distSlop 0.6 angleSlop 40.0 intraMol false intraRes
> false reveal true log true
    
    
    Constraints relaxed by 0.6 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false intraModel false distSlop 0.9 angleSlop 40.0 intraMol false intraRes
> false reveal true log true
    
    
    Constraints relaxed by 0.9 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 intraMol false intraRes false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> ~label hbond

> label delete hbond

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label delete

> ~hbonds

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false intraMol false intraRes false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false saltOnly true intraMol false intraRes false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 30.0 saltOnly true intraMol false intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 30 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false distSlop 0.5 angleSlop 40.0 saltOnly true intraMol false intraRes
> false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.5 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false distSlop 0.5 angleSlop 40.0 saltOnly true intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.5 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> label hbond color black

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label pseudobonds color black height 1.2

> label pseudobonds color black height 0.5

> select clear

> label pseudobonds offset 0,0.5,0

> label pseudobonds offset 0,0.4,0

> label pseudobonds offset 0,0.9,0

> label pseudobonds offset 0,0.1,0

> label pseudobonds offset 0.5,0.1,0

> label pseudobonds offset -0.5,0.1,0

> label pseudobonds offset -0.5,-0.4,0

> label pseudobonds offset -0.7,-0.4,0

> label pseudobonds offset -0.7,-0.9,0

> label pseudobonds offset -0.9,-0.9,0

> label pseudobonds offset -1.2,-0.9,0

> label pseudobonds offset -1.2,-0.9,0.5

> label pseudobonds text {dist:.2f}

> undo

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true
> log true

Atom specifier selects no atoms  

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> label pseudobonds text @length format %.2f

Expected a keyword  

> label pseudobonds text {0.length:.2f}

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> label pseudobonds text ""{0.length:.2f} Å""

> label pseudobonds color black height 0.5

> label pseudobonds offset -1.2,-0.9,0.5

> label pseudobonds color grey

> select clear

> label pseudobonds text ""{0.length:.1f} Å""

> label pseudobonds offset -1.1,-0.9,0.5

> label pseudobonds offset -1.1,-0.7,0.5

> select #1/A:206@HH12

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 1 residue, 2 models selected  

> label (#!1 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label offset 0.6,0.3,1

> label delete

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> select clear

> select #1/A:KHS

47 atoms, 48 bonds, 1 residue, 1 model selected  

> hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel
> false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true
> log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 40 degrees
    Models used:
    	1 16Mar26_flip_KHS_QMR_refined.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1  16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK  16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11  3.355  2.883
    

  
1 hydrogen bonds found  

> label pseudobonds text ""{0.length:.1f} Å""

> label pseudobonds offset -1.1,-0.7,0.5

> label pseudobonds color grey height 0.5

> select #1/A:206@HH12

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 1 residue, 2 models selected  

> label (#!1 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label residues offset 0.6,0.3,1

> select clear

> save ACP_hbond.png width 2000 supersample 4


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,12
      Model Number: MXCV3ZE/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.4 (24G517)
      Kernel Version: Darwin 24.6.0
      Time since boot: 42 days, 12 hours, 9 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        P34w-20:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2
}}}
"	defect	new	normal		Unassigned									
