id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2884 OpenMM: Error initializing context: clGetDeviceIDs petrpachl@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.5.5-200.fc31.x86_64-x86_64-with-fedora-31-Thirty_One ChimeraX Version: 0.91 (2019-12-23) Description running isolde.py Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/petr/xray/DeoR/solv/DeoR-coot-21_refmac1.pdb DeoR-coot-21_refmac1.pdb title: \--- [more info...] Chain information for DeoR-coot-21_refmac1.pdb #1 --- Chain | Description A C D | No description available B | No description available E H | No description available F G | No description available > style sel stick Changed 11331 atom styles > hide sel atoms > show sel cartoons > show sel cartoons > nucleotides sel fill > style nucleic & sel stick Changed 1464 atom styles > rainbow sel > select clear > color byhetero > color sel byhetero > rainbow sel > color sel bychain > color sel byhetero > toolshed show ISOLDE > set selectionWidth 4 DeoR-coot-21_refmac1.pdb title: \--- [more info...] Chain information for DeoR-coot-21_refmac1.pdb --- Chain | Description 1.1/A 1.1/C 1.1/D | No description available 1.1/B | No description available 1.1/E 1.1/H | No description available 1.1/F 1.1/G | No description available Done loading forcefield Discarding unrecognised/unsupported data array /unknown/unknown230318/FOM W MTZ file either contains multiple crystal datasets or is a mini-MTZ file. Checking... WARNING: This MTZ file contains data from multiple crystals. Only the data from the first crystal will be used. If you wish to use the other data, please split your MTZ file into individual datasets (you can do this using tools from the PHENIX or CCP suites). > ui mousemode rightMode select > select /D:39@CD 1 atom, 1 model selected > select /D:39@CD 1 atom, 1 model selected > select clear > select clear > select clear > hide #1.3 models > show #1.3 models > hide #1.3 models > clipper spotlight radius 11.00 > clipper spotlight radius 10.00 > addh Summary of feedback from adding hydrogens to DeoR-coot-21_refmac1.pdb #1.1 --- warnings | Not adding hydrogens to /B ASP 56 CB because it is missing heavy- atom bond partners Not adding hydrogens to /B ARG 220 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for DeoR-coot-21_refmac1.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for DeoR-coot-21_refmac1.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for DeoR-coot-21_refmac1.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for DeoR-coot-21_refmac1.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for DeoR-coot-21_refmac1.pdb (#1.1) chain E; guessing termini instead 3 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B ASP 2, /C MET 1, /D MET 1, /E DA 1, /F DA 1, /G DA 1, /H DA 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /E DT 18, /F DT 18, /G DT 18, /H DT 18 Chain-final residues that are not actual C termini: /A ASP 312, /B ASP 312, /C ASP 312, /D ASP 312 1201 hydrogen bonds /A ASP 312 is not terminus, removing H atom from 'C' /B ASP 312 is not terminus, removing H atom from 'C' /C ASP 312 is not terminus, removing H atom from 'C' /D ASP 312 is not terminus, removing H atom from 'C' 10728 hydrogens added > select clear > select clear > show #1.1.2 target m > select clear > select /D:62@CA 1 atom, 1 model selected > select /D:62@CA 1 atom, 1 model selected > select #1.1 22059 atoms, 22395 bonds, 5 models selected Traceback (most recent call last): File ""/home/petr/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2676, in _start_sim_or_toggle_pause self.start_sim() File ""/home/petr/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2706, in start_sim sm.start_sim() File ""/home/petr/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 653, in start_sim sh.start_sim() File ""/home/petr/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1555, in start_sim self._prepare_sim() File ""/home/petr/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1516, in _prepare_sim integrator, platform, properties) File ""/home/petr/programy/chimerax-0.91/lib/python3.7/site- packages/simtk/openmm/app/simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/home/petr/programy/chimerax-0.91/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetDeviceIDs (-1) Exception: Error initializing context: clGetDeviceIDs (-1) File ""/home/petr/programy/chimerax-0.91/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. OpenGL version: 4.5 (Core Profile) Mesa 19.2.8 OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) OpenGL vendor: Intel Open Source Technology Center }}} " defect closed normal Third Party fixed Tom Goddard all ChimeraX