![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 3 years ago
#6017 closed defect (can't reproduce)
openmm.OpenMMException: Error initializing context: clCreateContext
| Reported by: | 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-4.15.0-166-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Trying to follow the ISOLDE tutorial "Diagnosing and rebuilding errors in a high-resolution cryo-EM model" simulation won't start:
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py", line 5210, in __init__
this = _openmm.new_Context(*args)
See log for complete Python traceback.
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
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl
Errors may have occurred when running pip:
pip standard error:
\---
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /home/christian/.local/share/ChimeraX/1.3/site-packages
sysconfig: /home/christian/.local/lib/python3.9/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /home/christian/.local/share/ChimeraX/1.3/site-packages
sysconfig: /home/christian/.local/lib/python3.9/site-packages
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /home/christian/.local/share/ChimeraX/include/python3.9/ChimeraX-
Clipper
sysconfig: /home/christian/.local/include/python3.9/ChimeraX-Clipper
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /home/christian/.local/share/ChimeraX/bin
sysconfig: /home/christian/.local/bin
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /home/christian/.local/share/ChimeraX
sysconfig: /home/christian/.local
WARNING: Additional context:
user = True
home = None
root = None
prefix = None
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /home/christian/.local/share/ChimeraX/include/python3.9/ChimeraX-
ISOLDE
sysconfig: /home/christian/.local/include/python3.9/ChimeraX-ISOLDE
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>
distutils: /home/christian/.local/share/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /home/christian/.local/include/python3.9/UNKNOWN
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./Downloads/ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl
Requirement already satisfied: ChimeraX-Core~=1.3rc202112010000 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3)
(1.3)
Requirement already satisfied: ChimeraX-Atomic~=1.31 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (1.31)
Requirement already satisfied: ChimeraX-AtomicLibrary~=4.2 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (4.2)
Collecting ChimeraX-Clipper~=0.17.0
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.17.0/ChimeraX_Clipper-0.17.0-cp39-cp39-manylinux_2_17_x86_64.whl
(44.5 MB)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (1.0)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.4)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.1)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.0.2)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.1)
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.6.5)
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.5)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0.2)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.7)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.2.2)
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.0.1)
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.13.7)
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.6.1)
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.1)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.0)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-MapSeries~=2.0->ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE
Successfully installed ChimeraX-Clipper-0.17.0 ChimeraX-ISOLDE-1.3
\---
Successfully installed ChimeraX-Clipper-0.17.0 ChimeraX-ISOLDE-1.3
Installed ChimeraX-Clipper (0.17.0)
Installed ChimeraX-ISOLDE (1.3)
> open /home/christian/heavy-data/RocCORmono-6hlu.pdb
Chain information for RocCORmono-6hlu.pdb #1
---
Chain | Description
B | No description available
> open /home/christian/Downloads/cryosparc_P79_J614__localfilter.mrc
Opened cryosparc_P79_J614__localfilter.mrc as #2, grid size 168,168,168, pixel
1.44, shown at level 0.0755, step 1, values float32
> ui tool show ISOLDE
> set selectionWidth 4
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
Matplotlib created a temporary config/cache directory at
/tmp/matplotlib-0anptk0n because the default path
(/home/christian/.config/matplotlib) is not a writable directory; it is highly
recommended to set the MPLCONFIGDIR environment variable to a writable
directory, in particular to speed up the import of Matplotlib and to better
support multiprocessing.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 19 residues in model #1 to IUPAC-IUB
standards.
Chain information for RocCORmono-6hlu.pdb
---
Chain | Description
1.2/B | No description available
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> addh hbond true
Summary of feedback from adding hydrogens to RocCORmono-6hlu.pdb #1.2
---
warnings | Not adding hydrogens to /B LYS 424 CG because it is missing heavy-
atom bond partners
Not adding hydrogens to /B LYS 443 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B LYS 470 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B LEU 487 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B ASN 488 CB because it is missing heavy-atom bond
partners
47 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B PRO 777 N; /B MET 814 SD
notes | No usable SEQRES records for RocCORmono-6hlu.pdb (#1.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: /B ASP 412
Chain-initial residues that are not actual N termini: /B LEU 487, /B VAL 606,
/B TYR 748, /B PHE 798
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /B GLU 940, /B ILE 473, /B
CYS 600, /B LEU 728, /B THR 791
356 hydrogen bonds
Adding 'H' to /B LEU 487
Adding 'H' to /B VAL 606
Adding 'H' to /B TYR 748
Adding 'H' to /B PHE 798
/B GLU 940 is not terminus, removing H atom from 'C'
3560 hydrogens added
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> volume #2 level 0.3507
> ui mousemode right "translate selected models"
> view matrix models #1.2,1,0,0,18.909,0,1,0,41.298,0,0,1,15.427
> view matrix models #1.2,1,0,0,17.615,0,1,0,39.905,0,0,1,13.523
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.95549,0.29431,0.020397,14.288,0.27988,-0.88244,-0.37812,75.245,-0.093285,0.367,-0.92553,120.13
> view matrix models
> #1.2,-0.76442,0.13893,0.62957,131.9,0.15941,-0.90545,0.39338,43.572,0.62469,0.40107,0.67,-30.267
> view matrix models
> #1.2,0.81528,-0.34676,0.46377,15.063,0.10951,0.87876,0.46454,7.3714,-0.56862,-0.32794,0.7544,82.705
> view matrix models
> #1.2,0.12287,0.97955,-0.1593,81.785,0.053077,0.1538,0.98667,-1.6827,0.991,-0.12969,-0.033093,-12.164
> view matrix models
> #1.2,0.80814,-0.5699,0.14876,37.609,-0.45687,-0.76593,-0.45235,140.34,0.37174,0.2976,-0.87934,78.99
> view matrix models
> #1.2,0.94036,0.32482,0.10105,10.52,-0.11203,0.015225,0.99359,14.984,0.3212,-0.94565,0.050707,57.578
> view matrix models
> #1.2,-0.6457,-0.76037,0.070045,170.95,-0.019647,0.10825,0.99393,5.1089,-0.76334,0.64041,-0.084834,125.85
> view matrix models
> #1.2,-0.98378,0.10379,0.14631,178.12,0.090297,-0.41821,0.90385,11.404,0.155,0.9024,0.40206,14.635
> view matrix models
> #1.2,-0.90807,0.3552,-0.22189,186.74,-0.18763,0.12863,0.97378,20.256,0.37443,0.9259,-0.050162,20.191
> view matrix models
> #1.2,-0.90094,0.34149,-0.26776,201.1,-0.22644,0.15641,0.96138,63.735,0.37018,0.92678,-0.063585,73.785
> view matrix models
> #1.2,0.16544,-0.98621,0.0052641,121.51,-0.38878,-0.060313,0.91935,84.462,-0.90636,-0.15415,-0.39339,223.95
> view matrix models
> #1.2,0.52469,-0.82098,-0.22514,99.909,-0.63548,-0.5537,0.53812,136.81,-0.56645,-0.13928,-0.81224,217.48
> view matrix models
> #1.2,-0.26268,-0.93095,0.25362,143.53,-0.9565,0.21668,-0.19533,189.05,0.12689,-0.2939,-0.94738,168.44
> view matrix models
> #1.2,-0.2765,-0.93331,0.22908,146.12,-0.87526,0.14614,-0.46105,198.15,0.39682,-0.32799,-0.8573,140.95
> ui mousemode right "translate selected models"
> view matrix models
> #1.2,-0.2765,-0.93331,0.22908,147.86,-0.87526,0.14614,-0.46105,215.77,0.39682,-0.32799,-0.8573,149.6
> view matrix models
> #1.2,-0.2765,-0.93331,0.22908,150.39,-0.87526,0.14614,-0.46105,227.39,0.39682,-0.32799,-0.8573,147.54
> ui tool show "Fit in Map"
Fit molecule RocCORmono-6hlu.pdb (#1.2) to map
cryosparc_P79_J614__localfilter.mrc (#2) using 7291 atoms
average map value = 0.328, steps = 112
shifted from previous position = 5.45
rotated from previous position = 12.9 degrees
atoms outside contour = 4395, contour level = 0.3507
Position of RocCORmono-6hlu.pdb (#1.2) relative to
cryosparc_P79_J614__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
-0.35692766 -0.84664914 0.39469973 146.34283118
-0.90095781 0.20040834 -0.38485258 219.81131624
0.24673399 -0.49297234 -0.83432644 165.76255406
Axis -0.56566766 0.77413637 -0.28413550
Axis point 158.96206986 0.00000000 117.98874361
Rotation angle (degrees) 174.51597206
Shift along axis 40.28350268
> transparency 50
> transparency 0
> transparency 50
> view matrix models
> #1.2,-0.35693,-0.84665,0.3947,120.87,-0.90096,0.20041,-0.38485,184.32,0.24673,-0.49297,-0.83433,183.53
> volume #2 level 0.4533
> view matrix models
> #1.2,-0.35693,-0.84665,0.3947,119.36,-0.90096,0.20041,-0.38485,216.73,0.24673,-0.49297,-0.83433,165.55
> view matrix models
> #1.2,-0.35693,-0.84665,0.3947,141.88,-0.90096,0.20041,-0.38485,224.16,0.24673,-0.49297,-0.83433,173.28
Fit molecule RocCORmono-6hlu.pdb (#1.2) to map
cryosparc_P79_J614__localfilter.mrc (#2) using 7291 atoms
average map value = 0.4509, steps = 248
shifted from previous position = 5.73
rotated from previous position = 66.2 degrees
atoms outside contour = 3891, contour level = 0.4533
Position of RocCORmono-6hlu.pdb (#1.2) relative to
cryosparc_P79_J614__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.28880212 -0.17850721 0.94060008 39.40252380
-0.95728576 -0.06825615 0.28097164 186.28795222
0.01404627 -0.98156827 -0.19059493 163.25145882
Axis -0.72186340 0.52976169 -0.44527047
Axis point 0.00000000 173.74649079 -7.03996610
Rotation angle (degrees) 119.01407614
Shift along axis -2.44607243
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 9 models selected
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 9 models selected
> ~select #1.1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 8 models selected
> ~select #1.3
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 7 models selected
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 9 models selected
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 9 models selected
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> hide #!1.2 models
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> hide #1.3 models
> show #!1.2 models
> select #1.2
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 6 models selected
> show #1.3 models
> ui mousemode right zoom
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 9 models selected
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 9 models selected
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 9 models selected
> clipper associate #2 toModel #1
Opened cryosparc_P79_J614__localfilter.mrc as #1.1.1.1, grid size 168,168,168,
pixel 1.44, shown at step 1, values float32
/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py:2021: RuntimeWarning: divide by zero
encountered in double_scalars
self.global_k = scaling_constant/ref_g
> lighting simple
> set bgColor white
> set silhouettes true
> ui mousemode right translate
> ui mousemode right zoom
> volume #1.1.1.1 level -0.7427
> ui mousemode right translate
> volume #1.1.1.1 level -0.2068
> volume #1.1.1.1 level -0.03288
> hide
> cartoon
> color bychain
> color byhetero
> transparency 50
> transparency 0
> transparency 50
> transparency 0
> volume #1.1.1.1 level -0.2035
> set silhouettes false
> volume #1.1.1.1 level 0.02109
> clipper spotlight radius 13.00
> clipper spotlight radius 14.00
> clipper spotlight radius 15.00
> clipper spotlight radius 16.00
> clipper spotlight radius 17.00
> volume #1.1.1.1 level 1.172
> volume #1.1.1.1 level 0.894
> volume #1.1.1.1 level 1.002
> set silhouettes false
> clipper spotlight radius 16.00
> clipper spotlight radius 15.00
> clipper spotlight radius 14.00
> clipper spotlight radius 13.00
> clipper spotlight radius 12.00
> delete ~protein
> hice HC
Unknown command: hice HC
> hide HC
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 13 models selected
> select #1
7291 atoms, 7366 bonds, 4 pseudobonds, 486 residues, 13 models selected
> isolde sim start sel
ISOLDE: stopped sim
Fetching CCD TYR_LL from http://ligand-
expo.rcsb.org/reports/T/TYR_LL/TYR_LL.cif
Fetching CCD PHE_LL from http://ligand-
expo.rcsb.org/reports/P/PHE_LL/PHE_LL.cif
Fetching CCD PHE_LEO2 from http://ligand-
expo.rcsb.org/reports/P/PHE_LEO2/PHE_LEO2.cif
Fetching CCD PHE_LFZW from http://ligand-
expo.rcsb.org/reports/P/PHE_LFZW/PHE_LFZW.cif
Fetching CCD TYR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/TYR_LEO2/TYR_LEO2.cif
Fetching CCD DAH from http://ligand-expo.rcsb.org/reports/D/DAH/DAH.cif
Fetching CCD TYR_LFZW from http://ligand-
expo.rcsb.org/reports/T/TYR_LFZW/TYR_LFZW.cif
Fetching CCD 5CR from http://ligand-expo.rcsb.org/reports/5/5CR/5CR.cif
Fetching CCD PRO_LL from http://ligand-
expo.rcsb.org/reports/P/PRO_LL/PRO_LL.cif
Fetching CCD ALA_LL from http://ligand-
expo.rcsb.org/reports/A/ALA_LL/ALA_LL.cif
Fetching CCD SER_LL_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif
Fetching CCD SER_LL from http://ligand-
expo.rcsb.org/reports/S/SER_LL/SER_LL.cif
Fetching CCD ALA_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ALA_LEO2/ALA_LEO2.cif
Fetching CCD SER_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif
Fetching CCD ALA_LFZW from http://ligand-
expo.rcsb.org/reports/A/ALA_LFZW/ALA_LFZW.cif
Fetching CCD CYS_LL_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif
Fetching CCD THR_LL_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif
Fetching CCD SER_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif
Fetching CCD CYS_LL from http://ligand-
expo.rcsb.org/reports/C/CYS_LL/CYS_LL.cif
Fetching CCD THR_LL from http://ligand-
expo.rcsb.org/reports/T/THR_LL/THR_LL.cif
Fetching CCD VAL_LL from http://ligand-
expo.rcsb.org/reports/V/VAL_LL/VAL_LL.cif
Fetching CCD SER_LEO2 from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2/SER_LEO2.cif
Fetching CCD CYS_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif
Fetching CCD THR_LSN3_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif
Fetching CCD SER_LFZW_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif
Fetching CCD SER_LFZW from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW/SER_LFZW.cif
Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif
Fetching CCD ASP_LL_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif
Fetching CCD ASN_LL from http://ligand-
expo.rcsb.org/reports/A/ASN_LL/ASN_LL.cif
Fetching CCD ASP_LL from http://ligand-
expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif
Fetching CCD PRO_LEO2 from http://ligand-
expo.rcsb.org/reports/P/PRO_LEO2/PRO_LEO2.cif
Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif
Fetching CCD CYS_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif
Fetching CCD ASP_LSN3_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif
Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif
Fetching CCD THR_LEO2_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif
Fetching CCD ILE_LL from http://ligand-
expo.rcsb.org/reports/I/ILE_LL/ILE_LL.cif
Fetching CCD LEU_LL from http://ligand-
expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif
Fetching CCD CYS_LEO2 from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2/CYS_LEO2.cif
Fetching CCD THR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2/THR_LEO2.cif
Fetching CCD VAL_LEO2 from http://ligand-
expo.rcsb.org/reports/V/VAL_LEO2/VAL_LEO2.cif
Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif
Fetching CCD PRO_LFZW from http://ligand-
expo.rcsb.org/reports/P/PRO_LFZW/PRO_LFZW.cif
Fetching CCD THR_LFZW_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif
Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif
Fetching CCD CYS_LFZW from http://ligand-
expo.rcsb.org/reports/C/CYS_LFZW/CYS_LFZW.cif
Fetching CCD THR_LFZW from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW/THR_LFZW.cif
Fetching CCD VAL_LFZW from http://ligand-
expo.rcsb.org/reports/V/VAL_LFZW/VAL_LFZW.cif
Fetching CCD MET_LL from http://ligand-
expo.rcsb.org/reports/M/MET_LL/MET_LL.cif
Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif
Fetching CCD MET_LEO2 from http://ligand-
expo.rcsb.org/reports/M/MET_LEO2/MET_LEO2.cif
Fetching CCD MET_LFZW from http://ligand-
expo.rcsb.org/reports/M/MET_LFZW/MET_LFZW.cif
Fetching CCD FME from http://ligand-expo.rcsb.org/reports/F/FME/FME.cif
Traceback (most recent call last):
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim
sm.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 105, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
See log for complete Python traceback.
> select #1
7307 atoms, 7383 bonds, 4 pseudobonds, 486 residues, 19 models selected
> isolde sim start sel
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/cmd/cmd.py", line 103, in isolde_sim
isolde.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim
sm.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 105, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
Error processing trigger "changes":
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
> select #1
7307 atoms, 7383 bonds, 4 pseudobonds, 486 residues, 19 models selected
> select #2
Nothing selected
> volume #1.1.1.1 level 1.309
> volume #1.1.1.1 level 1.355
> volume #1.1.1.1 level 0.6939
> volume #1.1.1.1 level 0.9447
> close
> isolde demo cryo_em_intro modelOnly true startIsolde false
6out.pdb title:
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]
Chain information for 6out.pdb #1
---
Chain | Description | UniProt
A | capsid protein VP1 | CAPSD_NVN68
B | capsid protein VP1 | CAPSD_NVN68
C | capsid protein VP1 | CAPSD_NVN68
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB
standards.
6out.pdb title:
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]
Chain information for 6out.pdb
---
Chain | Description | UniProt
1.2/A | capsid protein VP1 | CAPSD_NVN68
1.2/B | capsid protein VP1 | CAPSD_NVN68
1.2/C | capsid protein VP1 | CAPSD_NVN68
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205
> open 20205 fromDatabase emdb
Summary of feedback from opening 20205 fetched from emdb
---
note | Fetching compressed map 20205 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz
Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32
> set bgColor black
> clipper associate #2 toModel #1
Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at step 1, values float32
> addh
Summary of feedback from adding hydrogens to 6out.pdb #1.2
---
notes | No usable SEQRES records for 6out.pdb (#1.2) chain A; guessing termini
instead
No usable SEQRES records for 6out.pdb (#1.2) chain B; guessing termini instead
No usable SEQRES records for 6out.pdb (#1.2) chain C; guessing termini instead
Chain-initial residues that are actual N termini: /A ASP 29, /B THR 9, /C ASP
29
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: /A SER 520, /B ALA 519, /C
ALA 519
1438 hydrogen bonds
/A SER 520 is not terminus, removing H atom from 'C'
/B ALA 519 is not terminus, removing H atom from 'C'
/C ALA 519 is not terminus, removing H atom from 'C'
11443 hydrogens added
> hide HC
> isolde restrain ligands #1
> select #1
22948 atoms, 23065 bonds, 1720 residues, 14 models selected
> isolde sim start sel
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/cmd/cmd.py", line 103, in isolde_sim
isolde.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim
sm.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 105, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
See log for complete Python traceback.
> isolde sim start sel
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/cmd/cmd.py", line 103, in isolde_sim
isolde.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim
sm.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "/home/christian/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 105, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__
this = _openmm.new_Context(*args)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 390.144
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP Pavilion Gaming Laptop 15-cx0xxx
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 15G 7.4G 1.1G 145M 7.1G 7.8G
Swap: 2.0G 523M 1.5G
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)
Subsystem: Hewlett-Packard Company UHD Graphics 620 [103c:8477]
Kernel driver in use: i915
Locale: ('en_US', '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 (3)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → openmm.OpenMMException: Error initializing context: clCreateContext |
follow-up: 2 comment:2 by , 4 years ago
You’re using a laptop with a “hybrid” GPU architecture (a weak Intel GPU for lightweight stuff, the GTX 1050 for grunt work). Support for that in Linux has historically been a bit rough - albeit improved over what it used to be. Problem is that *both* GPUs provide OpenCL drivers... the error you’re getting (-5, corresponding to CL_OUT_OF_RESOURCES) suggests to me it’s trying to run on the Intel GPU rather than the Nvidia one. Could you try the command “isolde set gpuDevice 1” and then see if you can start a simulation?
comment:3 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Reported by Christian Galicia