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Opened 4 hours ago
Last modified 2 hours ago
#20165 assigned defect
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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 ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5100567192},{"value":99},{"value":122},{"value":1153027057780171488},{"value":1027},{"value":16189035935414362382},{"value":16189035935632442190},{"value":14757395258967641293},{"value":4294967286},{"value":5100567122},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8557778248},{"value":0},{"value":10},{"value":259},{"value":8540644128,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4325590576,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8501825536,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8501825536,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6695565384},"cpsr":{"value":1073745920},"fp":{"value":5100567264},"sp":{"value":5100567232},"esr":{"value":1442840704,"description":" 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Address size fault"},"pc":{"value":6695545708},"far":{"value":0}}},{"id":24580208,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":193}],"threadState":{"x":[{"value":6342209536},{"value":228407},{"value":6341672960},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":6342209536},"esr":{"value":1442840704,"description":" Address size 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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
> color (#!1 & sel) #a582ffff
> color (#!1 & sel) #a57fffff
> color (#!1 & sel) #a57affff
> color (#!1 & sel) #a579ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #a478ffff
> color (#!1 & sel) #a477ffff
> color (#!1 & sel) #a476ffff
> color (#!1 & sel) #a374ffff
> color (#!1 & sel) #a373ffff
> color (#!1 & sel) #a272ffff
> color (#!1 & sel) #a172ffff
> color (#!1 & sel) #9c71ffff
> color (#!1 & sel) #9a71ffff
> color (#!1 & sel) #9972ffff
> color (#!1 & sel) #a87bffff
> color (#!1 & sel) #b581ffff
> color (#!1 & sel) #b781ffff
> color (#!1 & sel) #b881ffff
> color (#!1 & sel) #b981ffff
> color (#!1 & sel) #bb81ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #c181ffff
> color (#!1 & sel) #c783ffff
> color (#!1 & sel) #cc83ffff
> color (#!1 & sel) #cd83ffff
> color (#!1 & sel) #cf84ffff
> color (#!1 & sel) #d485ffff
> color (#!1 & sel) #d885ffff
> color (#!1 & sel) #db86ffff
> color (#!1 & sel) #de86ffff
> color (#!1 & sel) #df86ffff
> color (#!1 & sel) #e086ffff
> color (#!1 & sel) #e185ffff
> color (#!1 & sel) #e385ffff
> color (#!1 & sel) #e484ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #e282ffff
> color (#!1 & sel) #db7bffff
[Repeated 1 time(s)]
> color (#!1 & sel) #dc7effff
> color (#!1 & sel) #e183ffff
> color (#!1 & sel) #e284ffff
> color (#!1 & sel) #e688ffff
> color (#!1 & sel) #eb8dffff
> color (#!1 & sel) #ec8effff
> color (#!1 & sel) #f092ffff
> color (#!1 & sel) #f192ffff
> color (#!1 & sel) #f495ffff
> color (#!1 & sel) #f697ffff
> color (#!1 & sel) #f899ffff
> color (#!1 & sel) #f99bffff
[Repeated 1 time(s)]
> color (#!1 & sel) #f89cffff
> color (#!1 & sel) #f59effff
> color (#!1 & sel) #f49effff
> color (#!1 & sel) #f39effff
> color (#!1 & sel) #efa0ffff
> color (#!1 & sel) #eea1ffff
> color (#!1 & sel) #eba6ffff
> color (#!1 & sel) #eaa7ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #e9a9ffff
> color (#!1 & sel) #e7aeffff
> color (#!1 & sel) #e6aeffff
> color (#!1 & sel) #e5aeffff
[Repeated 1 time(s)]
> color (#!1 & sel) #e4afffff
> color (#!1 & sel) #e5b0ffff
> color (#!1 & sel) #e6b2ffff
> color (#!1 & sel) #e6b3ffff
> color (#!1 & sel) #e7b5ffff
> color (#!1 & sel) #e8b6ffff
> color (#!1 & sel) #ebb8ffff
> color (#!1 & sel) #efbbffff
> color (#!1 & sel) #f0bcffff
> color (#!1 & sel) #efbdffff
> color (#!1 & sel) #edbdffff
> color (#!1 & sel) #ebbeffff
> color (#!1 & sel) #e8beffff
> color (#!1 & sel) #e5bfffff
> color (#!1 & sel) #dfbeffff
[Repeated 1 time(s)]
> color (#!1 & sel) #dcbeffff
> color (#!1 & sel) #dbbeffff
> color (#!1 & sel) #d6beffff
> color (#!1 & sel) #d3bdffff
> color (#!1 & sel) #cbbaffff
> color (#!1 & sel) #c8baffff
> color (#!1 & sel) #c2b7ffff
> color (#!1 & sel) #bfb6ffff
> color (#!1 & sel) #beb6ffff
> color (#!1 & sel) #bcb6ffff
> color (#!1 & sel) #bbb5ffff
> color (#!1 & sel) #bab5ffff
> color (#!1 & sel) #b7b4ffff
> color (#!1 & sel) #b6b3ffff
> color (#!1 & sel) #b4b3ffff
> color (#!1 & sel) #b2b2ffff
> color (#!1 & sel) #b1b2ffff
> color (#!1 & sel) #b0b3ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #afb3ffff
> color (#!1 & sel) #aeb4ffff
> color (#!1 & sel) #adb4ffff
[Repeated 2 time(s)]
> color (#!1 & sel) #aeb4ffff
> color (#!1 & sel) #b0b5ffff
> color (#!1 & sel) #b1b6ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #b2b7ffff
> color (#!1 & sel) #b3b8ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #b5b9ffff
> color (#!1 & sel) #b5baffff
> color (#!1 & sel) #b6baffff
> color (#!1 & sel) #b7bbffff
> color (#!1 & sel) #b7bcffff
> color (#!1 & sel) #b8bcffff
> color (#!1 & sel) #b9bdffff
> color (#!1 & sel) #babeffff
> color (#!1 & sel) #bcbfffff
> color (#!1 & sel) #bfc1ffff
> color (#!1 & sel) #c0c2ffff
> color (#!1 & sel) #bec0ffff
> color (#!1 & sel) #bbbcffff
> color (#!1 & sel) #babbffff
> color (#!1 & sel) #b9bbffff
> color (#!1 & sel) #b8baffff
> color (#!1 & sel) #b8b9ffff
> color (#!1 & sel) #b6b7ffff
> color (#!1 & sel) #b6b6ffff
> color (#!1 & sel) #b4b5ffff
> color (#!1 & sel) #b4b4ffff
> color (#!1 & sel) #b3b3ffff
> color (#!1 & sel) #b3b2ffff
> color (#!1 & sel) #b2b1ffff
> color (#!1 & sel) #b2b0ffff
> color (#!1 & sel) #b1aeffff
> color (#!1 & sel) #b1adffff
> color (#!1 & sel) #b0acffff
> color (#!1 & sel) #b0abffff
> color (#!1 & sel) #afa9ffff
> color (#!1 & sel) #aea8ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #aea7ffff
> color (#!1 & sel) #ada6ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #aca6ffff
> color (#!1 & sel) #aba5ffff
> 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)]
> color (#!1 & sel) #a4a4ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #a5a4ffff
> color (#!1 & sel) #a7a5ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #a9a5ffff
> color (#!1 & sel) #aaa6ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #aba6ffff
> color (#!1 & sel) #aca7ffff
> color (#!1 & sel) #ada7ffff
> color (#!1 & sel) #aca6ffff
> color (#!1 & sel) #aca5ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #aba4ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #aba3ffff
> color (#!1 & sel) #a9a0ffff
> color (#!1 & sel) #a99fffff
[Repeated 1 time(s)]
> color (#!1 & sel) #a99effff
> color (#!1 & sel) #a89effff
> color (#!1 & sel) #a89dffff
> 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
> color (#!1 & sel) #8a88ffff
> color (#!1 & sel) #8787ffff
> color (#!1 & sel) #8688ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #8588ffff
> color (#!1 & sel) #8489ffff
> color (#!1 & sel) #8389ffff
> color (#!1 & sel) #828affff
> color (#!1 & sel) #818affff
> color (#!1 & sel) #808bffff
> color (#!1 & sel) #7f8bffff
> color (#!1 & sel) #7e8dffff
> color (#!1 & sel) #7d8dffff
> color (#!1 & sel) #7c8effff
> color (#!1 & sel) #7b8effff
[Repeated 1 time(s)]
> color (#!1 & sel) #7a8effff
> color (#!1 & sel) #798fffff
> color (#!1 & sel) #788fffff
> color (#!1 & sel) #7590ffff
> color (#!1 & sel) #7490ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #7390ffff
[Repeated 2 time(s)]
> color (#!1 & sel) #7490ffff
> color (#!1 & sel) #7590ffff
> color (#!1 & sel) #768fffff
> color (#!1 & sel) #798dffff
> color (#!1 & sel) #7a89ffff
> color (#!1 & sel) #7a86ffff
> color (#!1 & sel) #7a81ffff
> color (#!1 & sel) #7a7dffff
> color (#!1 & sel) #7d79ffff
> color (#!1 & sel) #8078ffff
> color (#!1 & sel) #8377ffff
> color (#!1 & sel) #8477ffff
> color (#!1 & sel) #8675ffff
> color (#!1 & sel) #8774ffff
> color (#!1 & sel) #8a72ffff
> color (#!1 & sel) #8b70ffff
> color (#!1 & sel) #8c6fffff
> color (#!1 & sel) #8c6effff
> color (#!1 & sel) #8c6dffff
> color (#!1 & sel) #8c6cffff
> color (#!1 & sel) #8e67ffff
> color (#!1 & sel) #8f66ffff
> color (#!1 & sel) #8f65ffff
> color (#!1 & sel) #9065ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #9466ffff
> color (#!1 & sel) #9767ffff
> color (#!1 & sel) #9867ffff
> color (#!1 & sel) #9967ffff
> color (#!1 & sel) #9b67ffff
> color (#!1 & sel) #9d68ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #9e68ffff
> 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
> color (#!1 & sel) #ad7fffff
> color (#!1 & sel) #ae81ffff
> color (#!1 & sel) #ae82ffff
> 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
> color (#!1 & sel) #9e93ffff
> color (#!1 & sel) #9d92ffff
> color (#!1 & sel) #9a91ffff
> color (#!1 & sel) #9790ffff
> color (#!1 & sel) #958fffff
> color (#!1 & sel) #938fffff
[Repeated 1 time(s)]
> color (#!1 & sel) #948fffff
> color (#!1 & sel) #958fffff
> 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)]
> color (#!1 & sel) #9a91ffff
> 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
> color (#!1 & sel) #8293ffff
> color (#!1 & sel) #8094ffff
> color (#!1 & sel) #7f94ffff
> color (#!1 & sel) #7e94ffff
> color (#!1 & sel) #7c94ffff
> color (#!1 & sel) #7a95ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #7995ffff
> color (#!1 & sel) #7896ffff
> color (#!1 & sel) #7696ffff
[Repeated 1 time(s)]
> color (#!1 & sel) #7596ffff
> color (#!1 & sel) #7497ffff
> 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)]
> color (#!1 & sel) #6a9cffff
> 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
Change History (1)
comment:1 by , 2 hours ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
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Reported by Ayomide