![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#17315 closed defect (duplicate)
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
The following bug report has been submitted:
Platform: macOS-15.3.2-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
Current thread 0x00000001eb364840 (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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.stl._stl, lxml.builder (total: 62)
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"procRole" : "Background",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 95817,
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"build" : "24D81",
"releaseType" : "User"
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"codeSigningMonitor" : 1,
"incident" : "BA9FFCF3-63E0-45D4-B9DB-138C8BDF1EC5",
"pid" : 80918,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-30 18:49:04.7136 -0700",
"procStartAbsTime" : 17279734629671,
"procExitAbsTime" : 24874441894912,
"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":"AD62C989-3BC2-5446-B964-D7F4C1541558","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "57E2E92E-788D-38F3-DE32-34425F113112",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"vmRegionInfo" : "0x727272727272 is not in any region. Bytes after previous region: 20281640465011 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 39.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000101, 0x7272727272727272","rawCodes":[257,8246779703540740722],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"UNKNOWN_0x101 at 0x7272727272727272 -> 0x0000727272727272 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":80918},
"vmregioninfo" : "0x727272727272 is not in any region. Bytes after previous region: 20281640465011 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 39.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/fp/Downloads/8RVE_pocket27_8_98kcal/8rve-pdb-
> bundle2-protonated_protein_c_protein_c.pdb
> /Users/fp/Downloads/8RVE_pocket27_8_98kcal/8rve-pdb-
> bundle2-protonated_protein_c-docking_compounds_a_-8-98.mol2
Chain information for 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1
---
Chain | Description
C | No description available
D | No description available
E | No description available
F | No description available
Computing secondary structure
Opened 8rve-pdb-bundle2-protonated_protein_c-docking_compounds_a_-8-98.mol2
containing 1 structure (29 atoms, 32 bonds)
> ui tool show "Add Hydrogens"
> addh #2#!1
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/C MET 1 CA because it is missing heavy-atom bond partners
Not adding hydrogens to 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb
#1/C SER 2 CA because it is missing heavy-atom bond partners
Not adding hydrogens to 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb
#1/C THR 3 CA because it is missing heavy-atom bond partners
Not adding hydrogens to 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb
#1/C ARG 4 CA because it is missing heavy-atom bond partners
Not adding hydrogens to 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb
#1/C SER 5 CA because it is missing heavy-atom bond partners
1001 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/F PRO 24
N; 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/F PRO 46 N; 8rve-
pdb-bundle2-protonated_protein_c_protein_c.pdb #1/C PRO 263 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/D PRO 24 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/C PRO 18 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/F PRO 75 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/E PRO 18 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/C PRO 24 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/F PRO 57 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/E PRO 24 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/C PRO 46 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/D PRO 263 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/E PRO 46 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/F PRO 18 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/D PRO 18 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/E PRO 75 N; 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/E PRO 57 N
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb (#1) chain C; guessing termini
instead
No usable SEQRES records for 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb (#1) chain D; guessing termini
instead
No usable SEQRES records for 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb (#1) chain E; guessing termini
instead
No usable SEQRES records for 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb (#1) chain F; guessing termini
instead
Chain-initial residues that are actual N termini: 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/C MET 1, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/D MET 1, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/E MET 1, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/F MET 1
Chain-initial residues that are not actual N termini: 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/C LEU 124, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/D GLN 126
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/C GLU 341, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/C SER 47, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/D GLY 335, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/D ALA 43, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/E VAL 254, 8rve-pdb-
bundle2-protonated_protein_c_protein_c.pdb #1/F HIS 253
730 hydrogen bonds
Adding 'H' to 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/C LEU 124
Adding 'H' to 8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/D GLN 126
8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/C GLU 341 is not
terminus, removing H atom from 'C'
8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/D GLY 335 is not
terminus, removing H atom from 'C'
8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/E VAL 254 is not
terminus, removing H atom from 'C'
8rve-pdb-bundle2-protonated_protein_c_protein_c.pdb #1/F HIS 253 is not
terminus, removing H atom from 'C'
29 hydrogens added
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true
54 contacts
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> set bgColor white
> toolshed show
> label #1-3 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> ~label #1-3 residues
> label #1-3 text "{0.name} {0.number}{0.insertion_code}"
> ~label #1-3 residues
> show surfaces
> hide surfaces
> select
5241 atoms, 5238 bonds, 56 pseudobonds, 1026 residues, 4 models selected
> show sel surfaces
> hide sel surfaces
> contacts saveFile /Users/fp/Downloads/8RVE_pocket27_8_98kcal/contacts
> intraModel false intraMol false ignoreHiddenModels true
54 contacts
> contacts intraModel false intraMol false ignoreHiddenModels true reveal true
54 contacts
> contacts intraModel false intraMol false ignoreHiddenModels true reveal true
54 contacts
> contacts setAttrs true intraModel false intraMol false ignoreHiddenModels
> true select true reveal true
54 contacts
> contacts intraModel false intraMol false ignoreHiddenModels true select true
> reveal true
54 contacts
> contacts intraModel false intraMol false ignoreHiddenModels true select true
> reveal true
54 contacts
> contacts saveFile /Users/fp/Downloads/8RVE_pocket27_8_98kcal/contacts
> intraModel false intraMol false ignoreHiddenModels true select true reveal
> true
54 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true select true reveal true
54 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true select true reveal true
54 contacts
> label (#2#!1 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true select true
54 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true select true
54 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true
54 contacts
> select clear
> save "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Interactions.png"
> width 1344 height 850 supersample 3
> save /Users/fp/Downloads/8RVE_pocket27_8_98kcal/closeup.cxs
> select add #2
53 atoms, 56 bonds, 1 residue, 2 models selected
> show sel surfaces
> save "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim.png" width 1344
> height 850 supersample 3
> save "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
> open /Users/fp/Downloads/8RVE_pocket27_8_98kcal/closeup.cxs
opened ChimeraX session
> select add #2
53 atoms, 56 bonds, 1 residue, 2 models selected
> show sel surfaces
> save "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC Vim Interact
> surface.cxs"
> save "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 interact
> Surface.png" width 1344 height 850 supersample 3
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
opened ChimeraX session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC Vim Interact
> surface.cxs"
opened ChimeraX session
> select add #1
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 4 models selected
> show sel surfaces
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC Vim Interact
> surface.cxs" format session
opened ChimeraX session
> select add #2
53 atoms, 56 bonds, 1 residue, 2 models selected
> select add #2
53 atoms, 56 bonds, 1 residue, 2 models selected
> select add #2
53 atoms, 56 bonds, 1 residue, 2 models selected
> select add #1
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 5 models selected
> select add #2
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 9 models selected
> select add #3
5241 atoms, 5238 bonds, 56 pseudobonds, 1026 residues, 10 models selected
> select add #2
5241 atoms, 5238 bonds, 56 pseudobonds, 1026 residues, 10 models selected
> select subtract #3
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 9 models selected
> select add #2
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 9 models selected
> hide #!2 models
> show #!2 models
> select add #2
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 9 models selected
> hide #!2 models
> select add #2
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 9 models selected
> show #!2 models
> hide sel atoms
> show sel surfaces
> select clear
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC Vim Interact
> surface.cxs" format session
opened ChimeraX session
> select
5241 atoms, 5238 bonds, 56 pseudobonds, 1026 residues, 6 models selected
> show sel surfaces
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie10.mp4
Movie saved to /Users/fp/Desktop/movie10.mp4
> color bychain
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie11.mp4
Movie saved to /Users/fp/Desktop/movie11.mp4
> color #2 #00d603ff
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie12.mp4
Movie saved to /Users/fp/Desktop/movie12.mp4
> hide surfaces
> save /Users/fp/Desktop/image3.png supersample 3
> select add #2
53 atoms, 56 bonds, 1 residue, 2 models selected
> show sel surfaces
> save /Users/fp/Desktop/image4.png supersample 3
> select add #1
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 6 models selected
> show sel surfaces
> save /Users/fp/Desktop/image5.png supersample 3
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
> format session
opened ChimeraX session
> color sel bychain
> color #2 #08d605ff
> select add #1
5241 atoms, 5238 bonds, 2 pseudobonds, 1026 residues, 4 models selected
> select clear
> select add #1
5188 atoms, 5182 bonds, 2 pseudobonds, 1025 residues, 3 models selected
> color sel bychain
> select clear
> save /Users/fp/Desktop/image3.png supersample 3
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> save /Users/fp/Desktop/image3.png supersample 3
> show surfaces
> save /Users/fp/Desktop/image4.png supersample 3
> save "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/full Vim.cxs"
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie10.mp4
Movie saved to /Users/fp/Desktop/movie10.mp4
> ui tool show "Side View"
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC Vim Interact
> surface.cxs" format session
opened ChimeraX session
> close session
> open "/Users/fp/Downloads/Part Studio 1 (2).stl" format stl
Opened STL file Part Studio 1 (2).stl containing 9944 triangles
> close session
> open /Users/fp/Downloads/6bkx.pdb format pdb
6bkx.pdb title:
Novel modes of inhibition of wild-type IDH1: direct covalent modification of
HIS315 with CMPD1 [more info...]
Chain information for 6bkx.pdb #1
---
Chain | Description | UniProt
A B C | isocitrate dehydrogenase [nadp] cytoplasmic | IDHC_HUMAN 1-414
Non-standard residues in 6bkx.pdb #1
---
CA — calcium ion
DWP —
(6AS,7S,9R,10AS)-7,10A-dimethyl-8-oxo-2-(phenylamino)-5,6,6A,7,8,9,10,10A-octahydrobenzo[H]quinazoline-9-carbonitrile
ICT — isocitric acid
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
> format session
opened ChimeraX session
> select ::name="ASP"
280 atoms, 224 bonds, 56 residues, 1 model selected
> undo
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
> format session
opened ChimeraX session
> select ::name="ASN"
195 atoms, 158 bonds, 39 residues, 1 model selected
> ui tool show "Selection Inspector"
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
> format session
opened ChimeraX session
> select ::name="UNL"
53 atoms, 56 bonds, 1 residue, 1 model selected
> select clear
> select ::name="UNL"
53 atoms, 56 bonds, 1 residue, 1 model selected
> select clear
> select ::name="ASP"
280 atoms, 224 bonds, 56 residues, 1 model selected
> close session
> open /Users/fp/Downloads/8RVE_pocket27_8_98kcal/closeup.cxs format session
opened ChimeraX session
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
> format session
opened ChimeraX session
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> select /F
140 atoms, 139 bonds, 35 residues, 1 model selected
> select
54788 atoms, 54912 bonds, 16 pseudobonds, 13697 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> hide #!1 models
> show #!1 models
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.6 models
> hide #1.7 models
> hide #1.8 models
> hide #1.9 models
> select /0:214-466
1012 atoms, 1011 bonds, 253 residues, 1 model selected
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style ball
Changed 54788 atom styles
> hide cartoons
> hide atoms
> show surfaces
> hide surfaces
> show surfaces
> select
> /0/1/2/3/4/5/6/7/8/9/A/AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/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/c/d/e/f/g/h/i/j/k/l/m/n/o/p/q/r/s/t/u/v/w/x/y/z
54788 atoms, 54912 bonds, 16 pseudobonds, 13697 residues, 2 models selected
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> show surfaces
> close session
> open /Users/fp/Downloads/8rve-pdb-bundle/8rve-pdb-bundle1.pdb
Summary of feedback from opening /Users/fp/Downloads/8rve-pdb-bundle/8rve-pdb-
bundle1.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STRUCTURAL PROTEIN 2024-02-01 XXXX
Chain information for 8rve-pdb-bundle1.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R S t | No description available
T | No description available
U p | No description available
V m | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
n | No description available
o | No description available
q | No description available
r | No description available
s | No description available
u | No description available
v | No description available
w x | No description available
y | No description available
z | No description available
> close session
> open /Users/fp/Downloads/8rve-pdb-bundle/8rve-pdb-bundle2.pdb
Summary of feedback from opening /Users/fp/Downloads/8rve-pdb-bundle/8rve-pdb-
bundle2.pdb
---
warning | Ignored bad PDB record found on line 1
HEADER STRUCTURAL PROTEIN 2024-02-01 XXXX
Chain information for 8rve-pdb-bundle2.pdb #1
---
Chain | Description
k y | No description available
l | No description available
m | No description available
n | No description available
o v | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
w | No description available
x | No description available
z | No description available
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> ui tool show "Selection Inspector"
> ui tool show "Side View"
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> hide atoms
> show cartoons
> select /a
836 atoms, 835 bonds, 209 residues, 1 model selected
> select /s
1108 atoms, 1106 bonds, 1 pseudobond, 277 residues, 2 models selected
> select: a, b, s, t
Unknown command: select: a, b, s, t
> select: a, b, s, t
Unknown command: select: a, b, s, t
> select /a:409
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /s:104
4 atoms, 3 bonds, 1 residue, 1 model selected
Drag select of 49 residues
Drag select of 61 residues
> select /a:214-422
836 atoms, 835 bonds, 209 residues, 1 model selected
> select /b:215-419
820 atoms, 819 bonds, 205 residues, 1 model selected
> show #!1 target m
> hide #!1 models
> show #!1 models
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> hide atoms
> show cartoons
> color bychain
> rainbow
> color bychain
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC017 Vim Overview.cxs"
> format session
opened ChimeraX session
> select #1/E
1287 atoms, 1286 bonds, 254 residues, 1 model selected
> select #1/D
1280 atoms, 1278 bonds, 1 pseudobond, 253 residues, 2 models selected
> close session
> open /Users/fp/Downloads/MXC017_27Pockets.pdb
Chain information for MXC017_27Pockets.pdb #1
---
Chain | Description
C | No description available
D | No description available
E | No description available
F | No description available
Computing secondary structure
> close session
> open /Users/fp/Downloads/MXC017_Vim_8.48kcal/8rve-pdb-
> bundle2-protonated_protein_c_protein_c-protonated-
> docking_compounds_a_nl1-1.pdb /Users/fp/Downloads/MXC017_Vim_8.48kcal/8rve-
> pdb-bundle2-protonated_protein_c_protein_c-protonated_protein_c.pdb
Chain information for 8rve-pdb-bundle2-protonated_protein_c_protein_c-
protonated_protein_c.pdb #2
---
Chain | Description
C | No description available
D | No description available
E | No description available
F | No description available
Computing secondary structure
> color bychain
> show surfaces
> hide surfaces
> style sphere
Changed 5215 atom styles
> style stick
Changed 5215 atom styles
> select ::name="NL1"
29 atoms, 32 bonds, 1 residue, 1 model selected
> show sel surfaces
> color #1 #00eb05ff
> color #1 #00eb07ff
> lighting full
> lighting soft
> lighting simple
> lighting full
> save /Users/fp/Downloads/MXC017_Vim_8.48kcal/full_2A2B_1A1B_MXC017.cxs
> save /Users/fp/Downloads/MXC017_Vim_8.48kcal/Fullassembly.png width 1344
> height 850 supersample 3
> hide sel surfaces
> color sel byhetero
> ui tool show Contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true
45 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true reveal true
45 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true reveal true
45 contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true select true
45 contacts
> label (#!1-2 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> select clear
> save /Users/fp/Downloads/MXC017_Vim_8.48kcal/closeup_Binding.png width 1344
> height 850 supersample 3
> save /Users/fp/Downloads/MXC017_Vim_8.48kcal/closeupbinding.cxs
> select
5215 atoms, 5212 bonds, 47 pseudobonds, 1026 residues, 6 models selected
> show sel surfaces
> color sel bychain
> color #1 #09eb1fff
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie11.mp4
Movie saved to /Users/fp/Desktop/movie11.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie12.mp4
Movie saved to /Users/fp/Desktop/movie12.mp4
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> hide surfaces
> show cartoons
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 54788 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> close session
> open /Users/fp/Downloads/MXC017_Vim_8.48kcal/full_2A2B_1A1B_MXC017.cxs
> format session
No such file/path:
/Users/fp/Downloads/MXC017_Vim_8.48kcal/full_2A2B_1A1B_MXC017.cxs
> open "/Users/fp/Library/CloudStorage/Box-Box/Pajonk Lab New/Ling/NEW
> COMPOUNDS/Ling/Manuscript/MXC017_Vim_8.48kcal
> Docking/full_2A2B_1A1B_MXC017.cxs"
opened ChimeraX session
> select ::name="ARG"
515 atoms, 422 bonds, 103 residues, 1 model selected
> label (#!2 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> select clear
> ~label #1-2 residues
> select: Arg45
Unknown command: select: Arg45
> Select: Arg45
Unknown command: Select: Arg45
> help help:user
> Select: ARG45
Unknown command: Select: ARG45
> Select: 2.2ARG45
Unknown command: Select: 2.2ARG45
> Select:
Unknown command: Select:
> Select:
Unknown command: Select:
> close session
> open /Users/fp/Downloads/9a3r.cif
9a3r.cif title:
Vimentin intermediate filament tetramer [more info...]
Chain information for 9a3r.cif #1
---
Chain | Description
A B C D | Vimentin
Computing secondary structure
> save /Users/fp/Downloads/9a3r.pdb relModel #1
> color bychain
> save /Users/fp/Desktop/image3.png supersample 3
> close session
> open
> /Users/fp/Downloads/9A3R_MXC017_docked_pocket45_8.77kcal/9a3r-protonated_protein_a.pdb
> /Users/fp/Downloads/9A3R_MXC017_docked_pocket45_8.77kcal/9a3r-protonated-
> docking_compounds_a_nl1-1.mol2
Chain information for 9a3r-protonated_protein_a.pdb #1
---
Chain | Description
A B C D | No description available
Computing secondary structure
Opened 9a3r-protonated-docking_compounds_a_nl1-1.mol2 containing 1 structure
(29 atoms, 32 bonds)
> color bychain
> style ball
Changed 9431 atom styles
> style stick
Changed 9431 atom styles
> color byhetero
> color #2 #d6d06bff
> color byhetero
> ui tool show Contacts
> contacts resSeparation 5 intraModel false intraMol false ignoreHiddenModels
> true select true
50 contacts
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select clear
> save /Users/fp/Desktop/image3.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie12.mp4
Movie saved to /Users/fp/Desktop/movie12.mp4
> save /Users/fp/Desktop/image4.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie13.mp4
Movie saved to /Users/fp/Desktop/movie13.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie14.mp4
Movie saved to /Users/fp/Desktop/movie14.mp4
> show surfaces
> hide surfaces
> show surfaces
> hide surfaces
> select add #2
29 atoms, 32 bonds, 1 residue, 2 models selected
> show sel surfaces
> color #2 #00dd0fff
> save /Users/fp/Desktop/image3.png supersample 3
> close session
> open 8rve format mmcif fromDatabase pdb
8rve title:
Vimentin intermediate filament [more info...]
Chain information for 8rve #1
---
Chain | Description | UniProt
0 1 2 3 4 5 6 7 8 9 A AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP 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 c d e f g h i j k l m n o p q r s t u v w x y z | Vimentin | VIME_HUMAN 1-466
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fp/Desktop/movie12.mp4
Movie saved to /Users/fp/Desktop/movie12.mp4
> close session
> open "/Users/fp/Library/CloudStorage/Box-Box/Pajonk Lab New/Ling/NEW
> COMPOUNDS/Ling/Manuscript/MXC017_Vim_8.48kcal
> Docking/full_2A2B_1A1B_MXC017.cxs" format session
No such file/path: /Users/fp/Library/CloudStorage/Box-Box/Pajonk Lab
New/Ling/NEW COMPOUNDS/Ling/Manuscript/MXC017_Vim_8.48kcal
Docking/full_2A2B_1A1B_MXC017.cxs
> open /Users/fp/Downloads/9a3r.pdb format pdb
Chain information for 9a3r.pdb #1
---
Chain | Description
A B C D | No description available
> color bychain
> close session
> open "/Users/fp/Downloads/8RVE_pocket27_8_98kcal/MXC Vim Interact
> surface.cxs" format session
opened ChimeraX session
> close session
> open 3klt format mmcif fromDatabase pdb
3klt title:
Crystal structure of a vimentin fragment [more info...]
Chain information for 3klt #1
---
Chain | Description | UniProt
A B C D | Vimentin | VIME_HUMAN 263-334
Non-standard residues in 3klt #1
---
1PE — pentaethylene glycol (PEG400)
CA — calcium ion
P33 — 3,6,9,12,15,18-hexaoxaicosane-1,20-diol (heptaethylene glycol; PEG330)
P6G — hexaethylene glycol (polyethylene glycol PEG400)
PG4 — tetraethylene glycol
PGE — triethylene glycol
SM — samarium (III) ion
3klt mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> open "/Users/fp/Downloads/Mouse Restrainer -
> 4136993/files/Mouse_Restrainer.stl"
Opened STL file Mouse_Restrainer.stl containing 1616 triangles
> ui mousemode right "crop volume"
> view
> view orient
> view
> view orient
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> color bychain
> show surfaces
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> hide surfaces
> hide cartoons
> show surfaces
> style sphere
Changed 2399 atom styles
> show surfaces
> hide surfaces
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
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 - 89.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: Mac Studio
Model Identifier: Mac13,1
Model Number: MJMV3LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 16 days, 3 hours, 40 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2723QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2715Q:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 30.00Hz
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
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
narwhals: 1.32.0
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: 2.2.4
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.0.1
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
pyKVFinder: 0.7.3
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
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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