camera stereo: 'NoneType' object has no attribute 'opengl_buffer

[satyshur@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.49.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
running isolde and camera stereo for 3D stereo.

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde demo cryo_em_intro modelOnly true startIsolde false

isolde is provided by the uninstalled bundle ISOLDE version 1.3  

> ui tool show Updates

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/satyshur/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/satyshur/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX/include/python3.9/ChimeraX-
Clipper  
sysconfig: /home/satyshur/.local/include/python3.9/ChimeraX-Clipper  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX/bin  
sysconfig: /home/satyshur/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX  
sysconfig: /home/satyshur/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX/include/python3.9/ChimeraX-
ISOLDE  
sysconfig: /home/satyshur/.local/include/python3.9/ChimeraX-ISOLDE  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/satyshur/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 22.0.3 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/home/satyshur/Downloads/ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl  
Requirement already satisfied: ChimeraX-Atomic~=1.31 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (1.31)  
Requirement already satisfied: ChimeraX-Core~=1.3rc202112010000 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
ISOLDE==1.3) (1.3)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (1.0)  
Collecting ChimeraX-Clipper~=0.17.0  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.17.0/ChimeraX_Clipper-0.17.0-cp39-cp39-manylinux_2_17_x86_64.whl
(44.5 MB)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=4.2 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
ISOLDE==1.3) (4.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.4)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.6.5)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.0.2)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.7)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0.2)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.2.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.5)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.13.7)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (2.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-MapSeries~=2.0->ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.31->ChimeraX-
ISOLDE==1.3) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.31->ChimeraX-ISOLDE==1.3) (1.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
Successfully installed ChimeraX-Clipper-0.17.0 ChimeraX-ISOLDE-1.3  
\---  

Successfully installed ChimeraX-Clipper-0.17.0 ChimeraX-ISOLDE-1.3  
Installed ChimeraX-Clipper (0.17.0)  
Installed ChimeraX-ISOLDE (1.3)  

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Summary of feedback from opening 20205 fetched from emdb  
---  
note | Fetching compressed map 20205 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz  
  
Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> volume #2 level 0.2406

> 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 level 0.168, step 1, values float32  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  

> ui tool show ISOLDE

> set selectionWidth 4

Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1.2 to IUPAC-IUB
standards.  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> volume #1.1.1.1 level 0.1114

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | No usable SEQRES records for 6out.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for 6out.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for 6out.pdb (#1.2) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A ASP 29, /B THR 9, /C ASP
29  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A SER 520, /B ALA 519, /C
ALA 519  
1438 hydrogen bonds  
/A SER 520 is not terminus, removing H atom from 'C'  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11443 hydrogens added  
  

> hide HC

> isolde restrain ligands #1

> select #1

22948 atoms, 23065 bonds, 1720 residues, 14 models selected  

> select clear

> isolde sim start sel

No atoms selected!  

> select #1

22948 atoms, 23065 bonds, 1720 residues, 14 models selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop sel

Atoms argument is not required for this command. Ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 22 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  
ISOLDE: paused sim  

> cview /A:57

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> cview /B:57

> cview /A:57

> view stereo

Expected an objects specifier or a view name or a keyword  

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting simple

> set bgColor black

> select up

601 atoms, 609 bonds, 42 residues, 1 model selected  

> select up

7561 atoms, 7604 bonds, 563 residues, 1 model selected  

> select up

22948 atoms, 23065 bonds, 1720 residues, 1 model selected  

> select up

22948 atoms, 23065 bonds, 1720 residues, 3 models selected  

> select up

22948 atoms, 23065 bonds, 1720 residues, 4 models selected  

> select up

22948 atoms, 23065 bonds, 1720 residues, 4 models selected  

> camera stereo

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.  
  
'NoneType' object has no attribute 'opengl_buffer'  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 235, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1499, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1512, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 752, in draw  
self.draw_self(renderer, draw_pass)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 759, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 786, in _draw_geometry  
ds.activate_bindings(renderer)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1858, in activate_bindings  
bi.activate()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2455, in activate  
self.bind_shader_variable(buffer)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2467, in bind_shader_variable  
buf_id = buffer.opengl_buffer  
AttributeError: 'NoneType' object has no attribute 'opengl_buffer'  
  




OpenGL version: 3.3.0 NVIDIA 470.74
OpenGL renderer: Quadro K4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision Tower 7810
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-2609 v3 @ 1.90GHz
Cache Size: 15360 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            94G         10G        3.5G        385M         80G         83G
	Swap:          4.0G          0B        4.0G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK106GL [Quadro K4000] [10de:11fa] (rev a1)	
	Subsystem: Hewlett-Packard Company Device [103c:079c]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Reported by Ken Satyshur

[Tom Goddard]

Definitely a bug in how ChimeraX is switching from mono to stereo OpenGL context. You probably would not hit it if you were in stereo mode before you opened the data.

Sequential stereo is rarely used, so although this bug would probably be often hit when enabling stereo, no one is using it since the sequential stereo hardware is almost unobtainable for years now. This creates another problem that I have almost no way to test it. We have a machine that can in theory test it (with a Quadro P5000 on Windows), but I am rarely in the lab due to the pandemic to allow testing on that machine and I do not believe it has been tested in the past 2 years. This is all a long way of saying that it may be a while before I can fix this.

[Tom Goddard]

I tried to reproduce this for an hour even following the exact steps in this bug report using the ISOLDE cryoEM tutorial and I never was able to produce this error or any OpenGL error and the stereo worked correctly. My tests were on Windows 10 (vive.cgl.ucsf.edu, Quadro P6000). This bug report is on Linux. We do not have any Linux stereo system to test on.

[Tom Goddard]

Actually I think I should put in a fix for this error. I am reluctant because I have no way to test it. But the code is using Bindings._bound_attr_buffers which is a dictionary mapping shader program attribute ids to buffer objects and the code documents it to allow None for the buffer object, and the error is due to some code that activates the bindings which does not consider the None case.

[Tom Goddard]

Fixed.

Added check to make sure OpenGL code does not try to set shader variables with None buffers. Was not able to create a test case for this error.