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#6953 closed defect (duplicate)
Long atom spec crashes ChimeraX
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.4rc202205111743 (2022-05-11 17:43:38 UTC)
Description
Managing to kill ChimeraX dead when compositing a big command via the shell (to limit display of an AlphaFold prediction to only the experimentally-resolved residues)...
In the command line:
open 6yai
alphafold match #1
In the shell:
m = session.models.list()[0]
from chimerax.core.commands import run
for cid in m.chains.chain_ids:
residues = m.residues[m.residues.chain_ids==cid]
run(session, f'~cartoon #2/{cid}:{",".join(str(num) for num in residues.numbers)}')
# Kaboom. No crash report on restart
Log:
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
UCSF ChimeraX version: 1.4rc202205111743 (2022-05-11)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6yai
6yai title:
Clathrin with bound beta2 appendage of AP2 [more info...]
Chain information for 6yai #1
---
Chain | Description | UniProt
A B E H J K L M | Clathrin heavy chain | C0MHR2_PIG
C | Clathrin heavy chain | C0MHR2_PIG
D I N O | Clathrin light chain | F1S398_PIG
F | AP-2 complex subunit β | AP2B1_HUMAN
> alphafold match #1
2 UniProt ids do not have AlphaFold database models: C0MHR2 (chains
E,C,M,A,B,J,K,L,H), F1S398 (chains D,O,I,N)
1 AlphaFold model found using UniProt identifier: P63010 (chain F)
2 AlphaFold models found using sequence similarity searches: P49951 (chains
E,C,M,A,B,J,K,L,H), P09497 (chains D,O,I,N)
AlphaFold chains matching 6yai
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
F | AP2B1_HUMAN | P63010 | 0.63 | 219 | 233 | 100
D | CLCB_HUMAN | P09497 | 25.38 | 229 | 104 | 97
O | CLCB_HUMAN | P09497 | 5.07 | 229 | 59 | 97
I | CLCB_HUMAN | P09497 | 13.10 | 229 | 58 | 97
N | CLCB_HUMAN | P09497 | 27.77 | 229 | 80 | 97
E | CLH1_BOVIN | P49951 | 38.89 | 1630 | 726 | 100
C | CLH1_BOVIN | P49951 | 17.55 | 1630 | 513 | 100
M | CLH1_BOVIN | P49951 | 27.31 | 1630 | 518 | 100
A | CLH1_BOVIN | P49951 | 5.05 | 1630 | 379 | 100
B | CLH1_BOVIN | P49951 | 41.31 | 1630 | 468 | 100
J | CLH1_BOVIN | P49951 | 2.98 | 1630 | 165 | 100
K | CLH1_BOVIN | P49951 | 5.50 | 1630 | 257 | 100
L | CLH1_BOVIN | P49951 | 46.00 | 1630 | 548 | 100
H | CLH1_BOVIN | P49951 | 4.36 | 1630 | 236 | 100
Opened 14 AlphaFold models
> ui tool show Shell
OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: Notebook
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Installed Packages:
-: imerax-isolde
-.imerax-isolde: 1.4.dev0
-himerax-clipper: 0.18.0
-himerax-isolde: 1.4.dev0
-imerax-isolde: 1.4.dev0
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.18.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4rc202205111743
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.4.dev0
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 22.3.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.2.0
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (7)
follow-up: 1 comment:1 by , 3 years ago
comment:2 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Long atom spec crashes ChimeraX |
comment:3 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Hi Tristan,
This is a problem with the grako parser using deep recursion for these big specs -- which can exceed stack limits and cause a crash. Your recipe does not crash on my Mac but does on a Windows box, so they must have different stack limits. I will put you on the CC list for the ticket we already have open for this. There is a function, chimerax.atomic.concise_residue_spec(), that takes a residue list/collection and generates the shortest spec that it can that covers those residues (and no others). It's useful as something to mitigate this problem until we get it fixed, but also has the useful effect of generating more readable logged commands, so I would recommend using it even after the problem is fixed -- though in one-off code like here it would be nice if it weren't necessary.
I do have a couple of other tips for the code you wrote:
(1) You can index directly into session.models, i.e. session.models[0]
(2) Since you've already limited "residues" to a particular chain ID, you don't have to append any residue numbers to your command.
--Eric
comment:4 by , 3 years ago
I meant to mention that occasionally a crash will leave the QWebEngine running, hence the zombie process. I don't think this behavior is particularly reproducible -- when it crashed on the Windows box I used, it all crashed and a report-a-bug dialog appeared when I restarted.
Also, once daily builds and release candidates start being built from current source again, crash-report dialogs will not appear on Windows at all.
follow-up: 5 comment:5 by , 3 years ago
Thanks for the tips! I have a feeling that session.models wasn’t indexable when I first started (at least I hope so - would be embarrassing to have been doing it wrong all this time!) On point 2: there’s a method to my madness. The point here is that the experimental structure has many unmodelled residues in each chain (more than actually modelled, in fact) - what I wanted to do was whittle down the AF model representation to only the experimentally modelled ones. Worked out fine once I shifted to using just the Python interface. :)
Note:
See TracTickets
for help on using tickets.
Turns out that the reason I didn't get a crash report is that ChimeraX was still running as a zombie process, but the GUI was dead. Found out that? when uninstalling in preparation for installing the new daily build - didn't notice any error message in the uninstall itself (and it removed both the Start Menu entry and the entry in the list of installed programs), but it didn't delete the actual C:\Program Files\ChimeraX directory contents. Seems like another possible bug there - does the uninstall not check to see if ChimeraX is running? Or was this just some glitch due to the unusual state of the ChimeraX process? ________________________________ From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: 25 May 2022 12:15 To: Tristan Croll <tic20@cam.ac.uk> Subject: [ChimeraX] #6953: ChimeraX bug report submission #6953: ChimeraX bug report submission ---------------------------+----------------------------- Reporter: Tristan Croll | Type: defect Status: new | Priority: normal Component: Unassigned | Blocked By: Blocking: | Notify when closed: ---------------------------+----------------------------- {{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.4rc202205111743 (2022-05-11 17:43:38 UTC) Description Managing to kill ChimeraX dead when compositing a big command via the shell (to limit display of an AlphaFold prediction to only the experimentally-resolved residues)... In the command line: open 6yai alphafold match #1 In the shell: m = session.models.list()[0] from chimerax.core.commands import run for cid in m.chains.chain_ids: residues = m.residues[m.residues.chain_ids==cid] run(session, f'~cartoon #2/{cid}:{",".join(str(num) for num in residues.numbers)}') # Kaboom. No crash report on restart Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.4rc202205111743 (2022-05-11) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6yai 6yai title: Clathrin with bound beta2 appendage of AP2 [more info...] Chain information for 6yai #1 --- Chain | Description | UniProt A B E H J K L M | Clathrin heavy chain | C0MHR2_PIG C | Clathrin heavy chain | C0MHR2_PIG D I N O | Clathrin light chain | F1S398_PIG F | AP-2 complex subunit β | AP2B1_HUMAN > alphafold match #1 2 UniProt ids do not have AlphaFold database models: C0MHR2 (chains E,C,M,A,B,J,K,L,H), F1S398 (chains D,O,I,N) 1 AlphaFold model found using UniProt identifier: P63010 (chain F) 2 AlphaFold models found using sequence similarity searches: P49951 (chains E,C,M,A,B,J,K,L,H), P09497 (chains D,O,I,N) AlphaFold chains matching 6yai --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id F | AP2B1_HUMAN | P63010 | 0.63 | 219 | 233 | 100 D | CLCB_HUMAN | P09497 | 25.38 | 229 | 104 | 97 O | CLCB_HUMAN | P09497 | 5.07 | 229 | 59 | 97 I | CLCB_HUMAN | P09497 | 13.10 | 229 | 58 | 97 N | CLCB_HUMAN | P09497 | 27.77 | 229 | 80 | 97 E | CLH1_BOVIN | P49951 | 38.89 | 1630 | 726 | 100 C | CLH1_BOVIN | P49951 | 17.55 | 1630 | 513 | 100 M | CLH1_BOVIN | P49951 | 27.31 | 1630 | 518 | 100 A | CLH1_BOVIN | P49951 | 5.05 | 1630 | 379 | 100 B | CLH1_BOVIN | P49951 | 41.31 | 1630 | 468 | 100 J | CLH1_BOVIN | P49951 | 2.98 | 1630 | 165 | 100 K | CLH1_BOVIN | P49951 | 5.50 | 1630 | 257 | 100 L | CLH1_BOVIN | P49951 | 46.00 | 1630 | 548 | 100 H | CLH1_BOVIN | P49951 | 4.36 | 1630 | 236 | 100 Opened 14 AlphaFold models > ui tool show Shell OpenGL version: 3.3.0 NVIDIA 497.29 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_GB.cp1252 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: windows Manufacturer: Notebook Model: P7xxTM1 OS: Microsoft Windows 10 Education (Build 19041) Memory: 68,654,501,888 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz OSLanguage: en-GB Installed Packages: -: imerax-isolde -.imerax-isolde: 1.4.dev0 -himerax-clipper: 0.18.0 -himerax-isolde: 1.4.dev0 -imerax-isolde: 1.4.dev0 alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.18.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4rc202205111743 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4.dev0 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.2 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pywin32: 303 pyzmq: 22.3.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.2.0 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 WMI: 1.5.1 }}} -- Ticket URL: 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