id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15527 glDrawBuffer: invalid operation chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-6.5.0-41-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.8 (2024-06-10 23:15:52 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: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > isolde tutorial > 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 B C | capsid protein VP1 | CAPSD_NVN68 9-520 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 1.2/B 1.2/C | capsid protein VP1 | CAPSD_NVN68 9-520 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > ui mousemode right select > select clear > open 20205 fromDatabase emdb Summary of feedback from opening 20205 fetched from emdb --- notes | Fetching compressed map 20205 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz Fetching map header 20205 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/header/emd-20205.xml Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.12, step 1, values float32, fit PDB 6out > 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 > set bgColor white > set bgColor black > set bgColor gray > set bgColor white > set bgColor gray > set bgColor black [Repeated 1 time(s)] > set bgColor gray > ui tool show ""Side View"" > select clear [Repeated 2 time(s)] > ui dockable false ISOLDE > addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records Termini for 6out.pdb (#1.2) chain B determined from SEQRES records Termini for 6out.pdb (#1.2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 Missing OXT added to C-terminal residue /A SER 520 1438 hydrogen bonds Adding 'H' to /A ASP 29 Adding 'H' to /C ASP 29 /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11439 hydrogens added > isolde restrain ligands #1 > ui tool show ""Ramachandran Plot"" [Repeated 2 time(s)] > select #1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > isolde sim start /A-C ISOLDE: started sim > isolde sim pause > view /A:57 > view /A:571 No objects specified. > view /A:57 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 23 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:57 ISOLDE: started sim > isolde sim pause > ui mousemode right select > select /A:58@CA 1 atom, 1 residue, 1 model selected > isolde pepflip /A:58 [Repeated 1 time(s)] > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > isolde pepflip /A:58 > isolde sim resume Unable to flip peptide bond after 50 rounds. Giving up. [Repeated 1 time(s)] > hbonds sel reveal true 1 hydrogen bonds found > select clear > hbonds reveal true 1514 hydrogen bonds found > ~hbonds > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /B:57 > view /C:57 > ui mousemode right select > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > isolde pepflip /C:58 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > ui mousemode right select > select clear > select /C:58@O 1 atom, 1 residue, 1 model selected > select clear > isolde sim start /A:375 ISOLDE: started sim > isolde sim pause > select clear > select up 24 atoms, 25 bonds, 1 residue, 2 models selected > isolde sim resume > select up 17 atoms, 17 bonds, 1 residue, 1 model selected > isolde sim pause > select clear > select up 17 atoms, 17 bonds, 1 residue, 1 model selected > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > ui tool show ""Ramachandran Plot"" > view /B:383 > volume gaussian #1 bfactor 150 Opened emdb 20205 gaussian as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at step 1, values float32 > clipper associate #2 toModel #1 Opened emdb 20205 gaussian as #1.1.1.2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at step 1, values float32 > hide #!1.1.1.2 models > show #!1.1.1.2 models > isolde sim start /B:381-383 ISOLDE: started sim > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > ui mousemode right pivot > ui mousemode right select > select clear [Repeated 3 time(s)] > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > isolde sim start /B:381-383 ISOLDE: started sim > isolde sim pause > isolde sim resume > isolde pepflip /B:382 Unable to flip peptide bond after 50 rounds. Giving up. > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > isolde pepflip /B:382 Unable to flip peptide bond after 50 rounds. Giving up. > isolde pepflip /B:382 > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > isolde pepflip /B:383 > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > isolde pepflip /B:383 > select clear > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > isolde pepflip /B:382 [Repeated 1 time(s)] > select up 593 atoms, 606 bonds, 41 residues, 2 models selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > isolde pepflip /B:382 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde pepflip /B:382 ISOLDE: started sim Unable to flip peptide bond after 50 rounds. Giving up. > select clear > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > isolde pepflip /B:382 Unable to flip peptide bond after 50 rounds. Giving up. > isolde pepflip /B:382 [Repeated 2 time(s)] > isolde cisflip /B:382 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:382 ISOLDE: started sim > isolde sim pause > isolde sim resume > isolde stepto first > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto > sb Unknown command: sb > sf Unknown command: sf > struts Missing or invalid ""atoms"" argument: empty atom specifier > isolde stepto > sf Unknown command: sf > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} > st > st first > st > view /A:73 > isolde sim start /A:30 ISOLDE: started sim > isolde sim pause > view /A:73 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:72-74 ISOLDE: started sim > select clear > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > view /A:101 > 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 > hbonds sel reveal true 3 hydrogen bonds found > select clear > hbonds reveal true 1517 hydrogen bonds found > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > isolde sim start /A:101 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > hbonds sel reveal true 20 hydrogen bonds found > ~hbonds > hbonds sel reveal true 20 hydrogen bonds found > view /A:106 > isolde sim start /A:106 ISOLDE: started sim > select clear > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > 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 > view /A:139 > isolde sim start #!1.2/A:139 ISOLDE: started sim > select clear > select up 19 atoms, 18 bonds, 1 residue, 2 models selected > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /A:175 > isolde sim start /A:175 ISOLDE: started sim > select clear > view /A:193 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /A:277 > isolde sim start /A:277 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /A:324 > isolde sim start /A:325 ISOLDE: started sim > isolde sim pause > isolde sim resume > select clear > view /A:330 > view /A:337 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:338 ISOLDE: started sim > isolde pepflip /A:338 [Repeated 1 time(s)] > isolde pepflip /A:340 [Repeated 1 time(s)] > isolde pepflip /A:339 > isolde pepflip /A:338 [Repeated 1 time(s)] > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > view /A:341 > isolde sim start /A:341 ISOLDE: started sim > select clear > view /A:345 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:345 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /A:353 > isolde sim start /A:345 ISOLDE: started sim > select clear [Repeated 1 time(s)] > isolde sim pause > select clear [Repeated 2 time(s)] > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > isolde sim start /A:353 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /A:364 > isolde sim start #!1.2/A:364 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /A:397 > volume gaussian #1.1.1.1 sDev 1.5 Opened emdb 20205 gaussian as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at step 1, values float32 > volume #2 level 0.03486 > volume #2 level 0.05842 > volume gaussian #1.1.1.1 sDev 1.5 Opened emdb 20205 gaussian as #3, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at step 1, values float32 > close #3 > close #2 > show #!1.1.1.1 models > hide #!1.1.1.1 models > show #!1.1.1.1 models > volume gaussian #1.1.1.1 sDev 1.5 Opened emdb 20205 gaussian as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at step 1, values float32 > show #!1.1.1.1 models > hide #!1.1.1.1 models > show #!1.1.1.1 models > hide #!1.1.1.1 models > show #!1.1.1.1 models > hide #!1.1.1.1 models > close #2 > view /A:409 > isolde sim start /A:409 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 /A:406-412 ISOLDE: started sim > isolde sim pause > view /A:412 > select clear > isolde sim resume > isolde sim pause > view /A:448 > 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 /A:412 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:448 ISOLDE: started sim > isolde sim pause > select clear > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 273, in _draw_scene draw_highlight_outline(r, highlight_drawings, color = self._highlight_color, File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1625, in draw_highlight_outline r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1927, in finish_rendering_outline r.pop_framebuffer() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 764, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 2313, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) > isolde sim start /A:448 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1306, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 21, in toolbar_command run(session, f'isolde sim start {_current_residue_sel_string(session)}') File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/cmd/cmd.py"", line 122, in isolde_sim isolde.start_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/isolde.py"", line 896, in start_sim sm.start_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 401, in start_sim sh.start_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1432, in start_sim self._prepare_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1377, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py"", line 5931, 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/python3.11/site-packages/openmm/openmm.py"", line 5931, in __init__ this = _openmm.new_Context(*args) ^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > style sel stick Changed 96 atom styles > select clear > isolde sim start Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1306, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 21, in toolbar_command run(session, f'isolde sim start {_current_residue_sel_string(session)}') File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/cmd/cmd.py"", line 122, in isolde_sim isolde.start_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/isolde.py"", line 896, in start_sim sm.start_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 401, in start_sim sh.start_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1432, in start_sim self._prepare_sim() File ""/home/xz/.local/share/ChimeraX/1.8/lib/python3.11/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1377, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py"", line 5931, 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/python3.11/site-packages/openmm/openmm.py"", line 5931, in __init__ this = _openmm.new_Context(*args) ^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 550.54.14 OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: ASUS Model: System Product Name OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 32 Intel(R) Core(TM) i9-14900K Cache Size: 36864 KB Memory: total used free shared buff/cache available Mem: 125Gi 4.3Gi 117Gi 138Mi 3.9Gi 120Gi Swap: 122Gi 0B 122Gi Graphics: 0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2684] (rev a1) Subsystem: ZOTAC International (MCO) Ltd. Device [19da:4675] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.6.2 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.3.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 distro: 1.9.0 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Graphics duplicate Tristan Croll all ChimeraX