id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17315	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
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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}
===== 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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX