Opened 3 years ago

Closed 3 years ago

#8117 closed defect (fixed)

Crash in OpenMM find_clashing_atoms()

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.80.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f2e9dea4740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5145 in getState
  File "/home/uqsbibby/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1627 in find_clashing_atoms
  File "/home/uqsbibby/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/validation/clashes.py", line 72 in populate_clash_table
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/shared/JEV G1/JEVG1_postprocess_masked.mrc"

Opened JEVG1_postprocess_masked.mrc as #1, grid size 650,650,650, pixel 0.8,
shown at step 1, values float32  

> volume #1 region 0,0,0,649,649,649 step 4

> open "/home/shared/JEV G1/JEVG1 homolgy model.pdb"

JEVG1 homolgy model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for JEVG1 homolgy model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open "/home/shared/JEV G1/JEVG1 homolgy model.pdb"

JEVG1 homolgy model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for JEVG1 homolgy model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "/home/shared/JEV G1/JEVG1 ASU.cxs"

Opened postprocess_masked.mrc as #2, grid size 650,650,650, pixel 0.8, shown
at level 0.011, step 2, values float32  
opened ChimeraX session  

> hide #!3 models

> show #1.1 models

> show #1.2 models

> show #1.3 models

> show #!2 models

> open /home/uqsbibby/Downloads/model_01.pdb

model_01.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model_01.pdb #4  
---  
Chain | Description  
C | No description available  
  

> matchmaker #4 to #1.3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ASU JEV1.pdb, chain U (#1.3) with model_01.pdb, chain C (#4),
sequence alignment score = 2326.2  
RMSD between 470 pruned atom pairs is 0.839 angstroms; (across all 500 pairs:
1.147)  
  

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> hide #1.2 models

> hide #1.1 models

> open /home/uqsbibby/Downloads/model_01.pdb

model_01.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model_01.pdb #5  
---  
Chain | Description  
C | No description available  
  

> matchmaker #5 to #1.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ASU JEV1.pdb, chain U (#1.2) with model_01.pdb, chain C (#5),
sequence alignment score = 2326.2  
RMSD between 470 pruned atom pairs is 0.839 angstroms; (across all 500 pairs:
1.147)  
  

> open /home/uqsbibby/Downloads/model_01.pdb

model_01.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model_01.pdb #6  
---  
Chain | Description  
C | No description available  
  

> matchmaker #6 to #1.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ASU JEV1.pdb, chain U (#1.1) with model_01.pdb, chain C (#6),
sequence alignment score = 2326.2  
RMSD between 470 pruned atom pairs is 0.839 angstroms; (across all 500 pairs:
1.147)  
  

> close #3

> fitmap #4 #5 #6 inMap #2

Fit molecules model_01.pdb (#4), model_01.pdb (#5), model_01.pdb (#6) to map
postprocess_masked.mrc (#2) using 11274 atoms  
average map value = 0.01178, steps = 44  
shifted from previous position = 0.1  
rotated from previous position = 0.0383 degrees  
atoms outside contour = 6538, contour level = 0.011049  
  
Position of model_01.pdb (#4) relative to postprocess_masked.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.30854319 0.63937062 0.70427716 -45.58237561  
-0.95114040 -0.19839837 -0.23657987 644.45696098  
-0.01153478 -0.74286156 0.66934569 285.62039744  
Axis -0.27876508 0.39413508 -0.87575542  
Axis point 164.85942721 401.46851642 0.00000000  
Rotation angle (degrees) 114.75871924  
Shift along axis 16.57625974  
  
Position of model_01.pdb (#5) relative to postprocess_masked.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.19401649 -0.97118177 -0.13843253 539.66350246  
0.92254473 0.13264698 0.36237551 -204.82381555  
-0.33356983 -0.19801702 0.92169432 143.17519283  
Axis -0.28238194 0.09832974 0.95424929  
Axis point 410.51026718 204.55449697 0.00000000  
Rotation angle (degrees) 82.86665936  
Shift along axis -35.90667496  
  
Position of model_01.pdb (#6) relative to postprocess_masked.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.30812729 -0.95133129 0.00513399 453.94536863  
0.95134508 0.30812092 -0.00200800 -118.82101181  
0.00032838 0.00550292 0.99998480 -36.10343296  
Axis 0.00394751 0.00252568 0.99998902  
Axis point 308.67494469 252.82278462 0.00000000  
Rotation angle (degrees) 72.05424108  
Shift along axis -34.61118546  
  

> fitmap #5 inMap #2

Fit molecule model_01.pdb (#5) to map postprocess_masked.mrc (#2) using 3758
atoms  
average map value = 0.01114, steps = 40  
shifted from previous position = 0.0547  
rotated from previous position = 0.207 degrees  
atoms outside contour = 2361, contour level = 0.011049  
  
Position of model_01.pdb (#5) relative to postprocess_masked.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.19620714 -0.97042548 -0.14063126 539.91751625  
0.92284746 0.13427190 0.36100362 -204.53001895  
-0.33144429 -0.20061269 0.92189979 142.95960386  
Axis -0.28307098 0.09617532 0.95426470  
Axis point 410.76011780 205.61807336 0.00000000  
Rotation angle (degrees) 82.75055161  
Shift along axis -36.08441753  
  

> fitmap #4 inMap #2

Fit molecule model_01.pdb (#4) to map postprocess_masked.mrc (#2) using 3758
atoms  
average map value = 0.01204, steps = 52  
shifted from previous position = 0.13  
rotated from previous position = 0.35 degrees  
atoms outside contour = 2087, contour level = 0.011049  
  
Position of model_01.pdb (#4) relative to postprocess_masked.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.30773617 0.63531501 0.70828898 -46.89574863  
-0.95143924 -0.19932223 -0.23459332 643.71624202  
-0.00786292 -0.74608678 0.66580229 286.77337258  
Axis -0.28189746 0.39469010 -0.87450189  
Axis point 162.99289824 401.99729781 0.00000000  
Rotation angle (degrees) 114.87424537  
Shift along axis 16.50436405  
  

> fitmap #6 inMap #2

Fit molecule model_01.pdb (#6) to map postprocess_masked.mrc (#2) using 3758
atoms  
average map value = 0.01236, steps = 64  
shifted from previous position = 0.123  
rotated from previous position = 0.35 degrees  
atoms outside contour = 2046, contour level = 0.011049  
  
Position of model_01.pdb (#6) relative to postprocess_masked.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.30983906 -0.95078901 -0.00011820 455.76614393  
0.95078891 0.30983896 0.00052337 -120.07367454  
-0.00046100 -0.00027454 0.99999986 -34.92553484  
Axis -0.00041961 0.00018027 0.99999990  
Axis point 310.58015283 253.89555940 0.00000000  
Rotation angle (degrees) 71.95047579  
Shift along axis -35.13842046  
  

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 25 residues in model #1.1 to IUPAC-IUB
standards.  
Done loading forcefield  

> select #6

3758 atoms, 3839 bonds, 500 residues, 1 model selected  

> ~select #6

Nothing selected  

> select #4

3758 atoms, 3839 bonds, 500 residues, 1 model selected  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 18 residues in model #4 to IUPAC-IUB
standards.  
model_01.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model_01.pdb  
---  
Chain | Description  
4.2/C | No description available  
  
Opened postprocess_masked.mrc as #4.1.1.1, grid size 650,650,650, pixel 0.8,
shown at step 1, values float32  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for ASU JEV1.pdb (#1.2) chain U; guessing
termini instead  
Chain-initial residues that are actual N termini: ASU JEV1.pdb #1.2/U PHE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: ASU JEV1.pdb #1.2/U ALA 500  
Chain-final residues that are not actual C termini:  
336 hydrogen bonds  
No usable SEQRES records for ASU JEV1.pdb (#1.3) chain U; guessing termini
instead  
Chain-initial residues that are actual N termini: ASU JEV1.pdb #1.3/U PHE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: ASU JEV1.pdb #1.3/U ALA 500  
Chain-final residues that are not actual C termini:  
336 hydrogen bonds  
No usable SEQRES records for model_01.pdb (#5) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: model_01.pdb #5/C PHE 218  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: model_01.pdb #5/C ALA 717  
Chain-final residues that are not actual C termini:  
386 hydrogen bonds  
No usable SEQRES records for model_01.pdb (#6) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: model_01.pdb #6/C PHE 218  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: model_01.pdb #6/C ALA 717  
Chain-final residues that are not actual C termini:  
386 hydrogen bonds  
No usable SEQRES records for ASU JEV1.pdb (#3.2) chain U; guessing termini
instead  
Chain-initial residues that are actual N termini: ASU JEV1.pdb #3.2/U PHE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: ASU JEV1.pdb #3.2/U ALA 500  
Chain-final residues that are not actual C termini:  
336 hydrogen bonds  
No usable SEQRES records for model_01.pdb (#4.2) chain C; guessing termini
instead  
Chain-initial residues that are actual N termini: model_01.pdb #4.2/C PHE 218  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: model_01.pdb #4.2/C ALA 717  
Chain-final residues that are not actual C termini:  
386 hydrogen bonds  
22200 hydrogens added  
  
ISOLDE: started sim  

> volume #4.1.1.1 level 0.008187

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #4.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #4.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 515.86.01
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           250G        7.3G        202G         57M         41G        242G
	Swap:          4.0G          0B        4.0G

Graphics:
	0000:17:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:37c4]	
	Kernel driver in use: nvidia
Locale: ('en_AU', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in OpenMM find_clashing_atoms()

comment:2 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

This would happen in 1.3 if the user hit the simulation stop button while the minimiser was still churning away trying to find a solution - the context would be invalidated before the failure-to-minimise callback ran, leading to a crash. No longer a problem - I abandoned the use of high simulation forces as a proxy for clashes in 1.4. It was always a bit problematic - since any serious clash will max out single-precision forces, the actual culprit preventing minimisation was almost never at the top of the list. The clash table now always uses the ChimeraX clash detection.

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