glDrawBuffer: invalid operation

[chimerax-bug-report@…]

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

[Tom Goddard]

This is a somewhat common Linux problem glDrawBuffer(GL_BACK) fails. In this report we see ISOLDE also can 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.

[Tom Goddard]

Corrected previous comment to say ISOLDE could not create an OpenCL context.