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
This is a somewhat common Linux problem glDrawBuffer(GL_BACK) fails. In this report we see ISOLDE also cannot create an OpenCL context. Not sure if that is a symptom of the same problem. Don't know what causes this, only ever seen on Linux (about 10-20 times), although I have long suspected that Linux may invalidate the OpenGL context for unknown reasons and we have no code to recover from that.