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Opened 17 months ago
Closed 17 months ago
#15384 closed defect (limitation)
ISOLDE: update coords: RuntimeError: clWaitForEvents
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/AW Lab/Desktop/Cryo-EM/8g1i.pdb"
8g1i.pdb title:
SPCAS9 with sgRNA and target DNA [more info...]
Chain information for 8g1i.pdb #1
---
Chain | Description | UniProt
A | crispr-associated endonuclease CAS9/CSN1 | CAS9_STRP1 1-1368
B | SGRNA |
C | DNA E2_TS |
D | DNA E2_NTS |
> open "C:/Users/AW Lab/Desktop/Cryo-EM/240526_SpCas9_WTsgRNA.cif"
Summary of feedback from opening C:/Users/AW Lab/Desktop/Cryo-
EM/240526_SpCas9_WTsgRNA.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 240526_SpCas9_WTsgRNA.cif #2
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ba | No description available
Bb Bc | No description available
Bd Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bi | No description available
Bj | No description available
Bk Cc | No description available
Ca | No description available
Cb | No description available
> style stick
Changed 23784 atom styles
> show cartoons
> hide atoms
> matchmaker #1 to #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 240526_SpCas9_WTsgRNA.cif, chain Ad (#2) with 8g1i.pdb, chain A
(#1), sequence alignment score = 1228
RMSD between 197 pruned atom pairs is 1.108 angstroms; (across all 306 pairs:
2.291)
> color #1 red
> color #2 #005500ff
> color #2 #ffaa00ff
> color #2 #0055ffff
> set bgColor white
> select #1:775-915
1122 atoms, 1133 bonds, 2 pseudobonds, 137 residues, 2 models selected
> select #1:775-917
1141 atoms, 1153 bonds, 2 pseudobonds, 139 residues, 2 models selected
> select #1:775-919
1161 atoms, 1173 bonds, 2 pseudobonds, 141 residues, 2 models selected
> select #1:775-921
1178 atoms, 1190 bonds, 2 pseudobonds, 143 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> open "C:/Users/AW Lab/Desktop/Cryo-EM/J247_003_volume_map_sharp.mrc"
Opened J247_003_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.23,
shown at level 0.118, step 1, values float32
> volume #3 level 0.1832
> hide #!2 models
> volume #3 level 0.216
> clipper associate #3 toModel #1
Opened J247_003_volume_map_sharp.mrc as #1.1.1.1, grid size 256,256,256, pixel
1.23, shown at level 0.432, step 1, values float32
8g1i.pdb title:
SPCAS9 with sgRNA and target DNA [more info...]
Chain information for 8g1i.pdb
---
Chain | Description | UniProt
1.2/A | crispr-associated endonuclease CAS9/CSN1 | CAS9_STRP1 1-1368
1.2/B | SGRNA |
1.2/C | DNA E2_TS |
1.2/D | DNA E2_NTS |
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Ba C 1 P
because it is missing heavy-atom bond partners
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Bb C 0 P because it is
missing heavy-atom bond partners
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Bc C 0 P because it is
missing heavy-atom bond partners
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Bd C 0 P because it is
missing heavy-atom bond partners
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Be C 0 P because it is
missing heavy-atom bond partners
12 messages similar to the above omitted
notes | No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Aa;
guessing termini instead
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ab; guessing
termini instead
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ac; guessing
termini instead
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ad; guessing
termini instead
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ae; guessing
termini instead
16 messages similar to the above omitted
Chain-initial residues that are actual N termini: 240526_SpCas9_WTsgRNA.cif
#2/Aa ILE 15, 240526_SpCas9_WTsgRNA.cif #2/Ab VAL 1091,
240526_SpCas9_WTsgRNA.cif #2/Ac LYS 962, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU
283, 240526_SpCas9_WTsgRNA.cif #2/Ae ILE 1128, 240526_SpCas9_WTsgRNA.cif #2/Af
ILE 687, 240526_SpCas9_WTsgRNA.cif #2/Ag ASP 715
Chain-initial residues that are not actual N termini:
240526_SpCas9_WTsgRNA.cif #2/Aa ALA 58, 240526_SpCas9_WTsgRNA.cif #2/Aa GLU
133, 240526_SpCas9_WTsgRNA.cif #2/Aa GLY 174, 240526_SpCas9_WTsgRNA.cif #2/Aa
ASP 190, 240526_SpCas9_WTsgRNA.cif #2/Ab GLY 1173, 240526_SpCas9_WTsgRNA.cif
#2/Ab LEU 1265, 240526_SpCas9_WTsgRNA.cif #2/Ad THR 321,
240526_SpCas9_WTsgRNA.cif #2/Ad GLU 435, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU
521, 240526_SpCas9_WTsgRNA.cif #2/Ad THR 568, 240526_SpCas9_WTsgRNA.cif #2/Ad
PHE 595, 240526_SpCas9_WTsgRNA.cif #2/Ad ASP 622, 240526_SpCas9_WTsgRNA.cif
#2/Ad LEU 624, 240526_SpCas9_WTsgRNA.cif #2/Ad TYR 664,
240526_SpCas9_WTsgRNA.cif #2/Af GLY 725
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 240526_SpCas9_WTsgRNA.cif
#2/Aa PHE 193, 240526_SpCas9_WTsgRNA.cif #2/Aa ASN 54,
240526_SpCas9_WTsgRNA.cif #2/Aa ILE 126, 240526_SpCas9_WTsgRNA.cif #2/Aa PHE
172, 240526_SpCas9_WTsgRNA.cif #2/Aa ASP 188, 240526_SpCas9_WTsgRNA.cif #2/Ab
GLY 1375, 240526_SpCas9_WTsgRNA.cif #2/Ab LYS 1163, 240526_SpCas9_WTsgRNA.cif
#2/Ab LYS 1252, 240526_SpCas9_WTsgRNA.cif #2/Ac LYS 1008,
240526_SpCas9_WTsgRNA.cif #2/Ad ILE 678, 240526_SpCas9_WTsgRNA.cif #2/Ad ASN
317, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU 431, 240526_SpCas9_WTsgRNA.cif #2/Ad
HIS 519, 240526_SpCas9_WTsgRNA.cif #2/Ad TYR 529, 240526_SpCas9_WTsgRNA.cif
#2/Ad GLU 574, 240526_SpCas9_WTsgRNA.cif #2/Ad ILE 609,
240526_SpCas9_WTsgRNA.cif #2/Ad ASP 622, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU
659, 240526_SpCas9_WTsgRNA.cif #2/Ae LYS 1132, 240526_SpCas9_WTsgRNA.cif #2/Af
ILE 767, 240526_SpCas9_WTsgRNA.cif #2/Af ASN 698, 240526_SpCas9_WTsgRNA.cif
#2/Ag LYS 718
710 hydrogen bonds
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa ALA 58
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa GLU 133
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa GLY 174
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa ASP 190
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Ab GLY 1173
10 messages similar to the above omitted
240526_SpCas9_WTsgRNA.cif #2/Aa PHE 193 is not terminus, removing H atom from
'C'
240526_SpCas9_WTsgRNA.cif #2/Ab GLY 1375 is not terminus, removing H atom from
'C'
240526_SpCas9_WTsgRNA.cif #2/Ac LYS 1008 is not terminus, removing H atom from
'C'
240526_SpCas9_WTsgRNA.cif #2/Ad ILE 678 is not terminus, removing H atom from
'C'
240526_SpCas9_WTsgRNA.cif #2/Ae LYS 1132 is not terminus, removing H atom from
'C'
2 messages similar to the above omitted
Termini for 8g1i.pdb (#1.2) chain A determined from SEQRES records
Termini for 8g1i.pdb (#1.2) chain B determined from SEQRES records
Termini for 8g1i.pdb (#1.2) chain C determined from SEQRES records
Termini for 8g1i.pdb (#1.2) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 8g1i.pdb #1.2/A LYS 4,
8g1i.pdb #1.2/A ALA 589, 8g1i.pdb #1.2/A SER 719, 8g1i.pdb #1.2/A VAL 922,
8g1i.pdb #1.2/A GLY 1030, 8g1i.pdb #1.2/A LYS 1059, 8g1i.pdb #1.2/A GLU 1253
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 8g1i.pdb #1.2/A ILE 580,
8g1i.pdb #1.2/A GLN 712, 8g1i.pdb #1.2/A ARG 765, 8g1i.pdb #1.2/A ASP 1012,
8g1i.pdb #1.2/A ILE 1050, 8g1i.pdb #1.2/A HIS 1241, 8g1i.pdb #1.2/A GLN 1364
Chain-initial residues that are not actual 5' termini: 8g1i.pdb #1.2/D DG 28
828 hydrogen bonds
Adding 'H' to 8g1i.pdb #1.2/A LYS 4
Adding 'H' to 8g1i.pdb #1.2/A ALA 589
Adding 'H' to 8g1i.pdb #1.2/A SER 719
Adding 'H' to 8g1i.pdb #1.2/A VAL 922
Adding 'H' to 8g1i.pdb #1.2/A GLY 1030
2 messages similar to the above omitted
8g1i.pdb #1.2/A GLN 1364 is not terminus, removing H atom from 'C'
8g1i.pdb #1.2/D DG 28 is not terminus, removing H atom from O5'
8g1i.pdb #1.2/C DA 31 is not terminus, removing H atom from O3'
20017 hydrogens added
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 80 residues in model #1.2 to IUPAC-IUB
standards.
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> ui tool show "Ramachandran Plot"
QWindowsWindow::setGeometry: Unable to set geometry 1920x1010+0+23 (frame:
1936x1049-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1009+0+23 (frame: 1936x1048-8-8) margins: 8, 31, 8, 8
minimum size: 454x1010 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=470, y=1049)))
> clipper spotlight
> select add #1.1.1
19 atoms, 1 residue, 6 models selected
> select subtract #1.1.1
19 atoms, 1 residue, 2 models selected
> select ~sel & ##selected
23581 atoms, 24112 bonds, 6 pseudobonds, 1296 residues, 2 models selected
> select ~sel & ##selected
19 atoms, 18 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
23581 atoms, 24112 bonds, 6 pseudobonds, 1296 residues, 2 models selected
> select ~sel & ##selected
19 atoms, 18 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
23581 atoms, 24112 bonds, 6 pseudobonds, 1296 residues, 2 models selected
> isolde restrain ligands #1
> select #1
23600 atoms, 24130 bonds, 6 pseudobonds, 1297 residues, 19 models selected
> isolde sim start #1.2/B,A,C-D
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #1.2/B,A,C-D
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #1.2/A:195
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> ui mousemode right "isolde tug residue"
> ui mousemode right "isolde tug selection"
> ui mousemode right "isolde tug residue"
> ui mousemode right "isolde tug atom"
> isolde tutorial
3 models selected
> view /A:5
> view /A:57
> isolde sim pause
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/A:1304
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #1.2
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #1.2/A:208
ISOLDE: started sim
> volume show
> transparency 50
> isolde sim pause
> isolde sim resume
> volume #1.1.1.1 level 0.356
> volume #1.1.1.1 level 0.165
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\delayed_reaction.py", line 81, in callback
self.ff(*self.ff_args)
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_update_coordinates_and_repeat
self.atoms.coords = th.coords
^^^^^^^^^
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords
return self.smoothed_coords
^^^^^^^^^^^^^^^^^^^^
RuntimeError: clWaitForEvents
Error processing trigger "new frame":
RuntimeError: clWaitForEvents
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords
return self.smoothed_coords
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> isolde sim pause
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/A:183
ISOLDE: started sim
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\delayed_reaction.py", line 81, in callback
self.ff(*self.ff_args)
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_update_coordinates_and_repeat
self.atoms.coords = th.coords
^^^^^^^^^
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords
return self.smoothed_coords
^^^^^^^^^^^^^^^^^^^^
RuntimeError: Error invoking kernel findBlocksWithInteractions:
clEnqueueNDRangeKernel (-5)
Error processing trigger "new frame":
RuntimeError: Error invoking kernel findBlocksWithInteractions:
clEnqueueNDRangeKernel (-5)
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords
return self.smoothed_coords
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2114
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.2
Locale: zh_HK.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: FUJITSU CLIENT COMPUTING LIMITED
Model: ESPRIMO D7011
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 33,877,090,304
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (2)
comment:1 by , 17 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: update coords: RuntimeError: clWaitForEvents |
comment:2 by , 17 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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Low-end GPU, returning CL_OUT_OF_RESOURCES.