Opened 4 years ago

Closed 3 years ago

Last modified 3 years ago

#6692 closed defect (duplicate)

Problem switching in/out of stereo: 'NoneType' object has no attribute 'opengl_buffer'

Reported by: satyshur@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.62.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open /home/satyshur/projects/keck/PriA-Cryo/PriA-PriB-tim/newmaps/chimera-
> isolde/first.cxs format session

Opened monomer_sharpened_scale_recentre.mrc as #2, grid size 192,192,192,
pixel 1.08, shown at level 0.144, step 1, values float32  
Opened fit_268.mrc as #3, grid size 192,192,192, pixel 1.08, shown at level
2.48, step 1, values float32  
Log from Fri Apr 22 14:43:29 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/satyshur/projects/keck/PriA-Cryo/PriA-PriB-tim/newmaps/chimera-
> isolde/EC20-rfn55DNA-tim-priB-PBF-coot-13.pdb

Summary of feedback from opening /home/satyshur/projects/keck/PriA-Cryo/PriA-
PriB-tim/newmaps/chimera-isolde/EC20-rfn55DNA-tim-priB-PBF-coot-13.pdb  
---  
warnings | End residue of secondary structure not found: SHEET 1 E 2 THR H 453
ALA H 455 0  
End residue of secondary structure not found: SHEET 1 L 2 HIS B 26 VAL B 30 0  
  
Chain information for EC20-rfn55DNA-tim-priB-PBF-coot-13.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
J | No description available  
Z | No description available  
  

> open /home/satyshur/projects/keck/PriA-Cryo/PriA-PriB-tim/newmaps/chimera-
> isolde/monomer_sharpened_scale_recentre.mrc

Opened monomer_sharpened_scale_recentre.mrc as #2, grid size 192,192,192,
pixel 1.08, shown at level 0.105, step 1, values float32  

> volume #2 level 0.144

> style stick

Changed 8974 atom styles  

> open /home/satyshur/projects/keck/PriA-Cryo/PriA-PriB-tim/newmaps/chimera-
> isolde/sharp_3p8.mrc

Opened sharp_3p8.mrc as #3, grid size 192,192,192, pixel 1.08, shown at level
0.0717, step 1, values float32  

> close #3

> open /home/satyshur/projects/keck/PriA-Cryo/PriA-PriB-tim/newmaps/chimera-
> isolde/fit_268.mrc

Opened fit_268.mrc as #3, grid size 192,192,192, pixel 1.08, shown at level
2.48, step 1, values float32  

> toolshed show

> save /home/satyshur/projects/keck/PriA-Cryo/PriA-PriB-tim/newmaps/chimera-
> isolde/first.cxs

——— End of log from Fri Apr 22 14:43:29 2022 ———

opened ChimeraX session  

> close #1

> open /home/satyshur/projects/keck/PriA-Cryo/PriA-PriB-tim/newmaps/chimera-
> isolde/EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb

Summary of feedback from opening /home/satyshur/projects/keck/PriA-Cryo/PriA-
PriB-tim/newmaps/chimera-isolde/EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb  
---  
warning | End residue of secondary structure not found: SHEET 1 E 2 THR H 453
ALA H 455 0  
  
Chain information for EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
J | No description available  
Z | No description available  
  

> style stick

Changed 8951 atom styles  

> clipper associate #2 toModel #1

Opened monomer_sharpened_scale_recentre.mrc as #1.1.1.1, grid size
192,192,192, pixel 1.08, shown at level 0.18, step 1, values float32  
Chain information for EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/J | No description available  
1.2/Z | No description available  
  

> volume #3 style mesh

> volume #3 color #e9b96e

> hide #!3 models

> start isolde

Unknown command: start isolde  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 82 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to EC20-rfn55DNA-tim-priB-NOPBF-
coot-15.pdb #1.2  
---  
warnings | Not adding hydrogens to /G DC 4 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /J DA 11 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb (#1.2)
chain G; guessing termini instead  
No usable SEQRES records for EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb (#1.2)
chain H; guessing termini instead  
No usable SEQRES records for EC20-rfn55DNA-tim-priB-NOPBF-coot-15.pdb (#1.2)
chain J; guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A THR 2, /B THR 2, /H ALA 2  
Chain-initial residues that are not actual N termini: /A LEU 87  
Chain-final residues that are actual C termini: /H GLY 732  
Chain-final residues that are not actual C termini: /A ILE 100, /A LYS 84, /B
GLU 98  
634 hydrogen bonds  
Adding 'H' to /A LEU 87  
/A ILE 100 is not terminus, removing H atom from 'C'  
/B GLU 98 is not terminus, removing H atom from 'C'  
8263 hydrogens added  
  

> hide HC

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started 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: Corrected atom nomenclature of 1 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: Corrected atom nomenclature of 1 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: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
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: started sim  
ISOLDE: paused sim  
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: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 0.06814

> volume #1.1.1.1 level 0.06124

> volume #1.1.1.1 level 0.09375

> volume #1.1.1.1 level 0.04932

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> camera stereo

> camera hardware stereo

Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword  

> camera mono

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 470.103.01
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        9.1G         67G        137M         17G         84G
	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

Change History (7)

comment:1 by pett, 3 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem switching in/out of stereo: 'NoneType' object has no attribute 'opengl_buffer'

Reported by Ken Satyshur

comment:2 by Tom Goddard, 3 years ago

Resolution: → duplicate
Status: assigned → closed

This was fixed 2 months ago in the daily builds when you reported the same error #6171. But the fix is not in the 6 month old ChimeraX 1.3 you are using.

in reply to:  3 ; comment:3 by kenneth.satyshur@…, 3 years ago 

OK thanks. I will use the daily builds.
kas



Kenneth A. Satyshur, M.S., Ph.D.

Senior Scientist,

College of Ag and Life Sciences: Department of Bacteriology;

School of Medicine and Public Health:

Departments of Biomolecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center

(Small Molecule Screening Facility)

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, April 27, 2022 1:37 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Kenneth Satyshur <kenneth.satyshur@wisc.edu>
Subject: Re: [ChimeraX] #6692: Problem switching in/out of stereo: 'NoneType' object has no attribute 'opengl_buffer'

#6692: Problem switching in/out of stereo: 'NoneType' object has no attribute
'opengl_buffer'
---------------------------------+-------------------------
          Reporter:  satyshur@…  |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Graphics    |    Version:
        Resolution:  duplicate   |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => duplicate


Comment:

 This was fixed 2 months ago in the daily builds when you reported the same
 error #6171.  But the fix is not in the 6 month old ChimeraX 1.3 you are
 using.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6692#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  4 ; comment:4 by kenneth.satyshur@…, 3 years ago 

I tried to install isolde and clipper into daily build

UCSF ChimeraX version: 1.4.dev202204270129 (2022-04-27)

centos7 version but got the following error and will not install:

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-Core~=1.3rc202112010000 in /usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (1.4.dev202204270129)
Requirement already satisfied: ChimeraX-Atomic~=1.31 in /usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (1.38.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.3) (1.0)
ERROR: Could not find a version that satisfies the requirement ChimeraX-AtomicLibrary~=4.2 (from chimerax-isolde) (from versions: none)
ERROR: No matching distribution found for ChimeraX-AtomicLibrary~=4.2
WARNING: You are using pip version 21.3.1; however, version 22.0.4 is available.
You should consider upgrading via the '/usr/libexec/UCSF-ChimeraX-daily/bin/ChimeraX -m pip install --upgrade pip' command.
I must go back to the 8 Dec stable release. Please advise.
thanks
kas



Kenneth A. Satyshur, M.S., Ph.D.

Senior Scientist,

College of Ag and Life Sciences: Department of Bacteriology;

School of Medicine and Public Health:

Departments of Biomolecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center

(Small Molecule Screening Facility)

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, April 27, 2022 1:37 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Kenneth Satyshur <kenneth.satyshur@wisc.edu>
Subject: Re: [ChimeraX] #6692: Problem switching in/out of stereo: 'NoneType' object has no attribute 'opengl_buffer'

#6692: Problem switching in/out of stereo: 'NoneType' object has no attribute
'opengl_buffer'
---------------------------------+-------------------------
          Reporter:  satyshur@…  |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Graphics    |    Version:
        Resolution:  duplicate   |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => duplicate


Comment:

 This was fixed 2 months ago in the daily builds when you reported the same
 error #6171.  But the fix is not in the 6 month old ChimeraX 1.3 you are
 using.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6692#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by Tom Goddard, 3 years ago

Cc: Tristan Croll added

Those messages suggest that ISOLDE does not work with the ChimeraX daily build. Maybe it only works with the current ChimeraX 1.3 release. ISOLDE is developed by Tristan Croll in Cambridge. If you report the installation error as a separate bug he can probably give an information about that. We have updated the Qt window toolkit that ChimeraX is based on in our daily builds from Qt 5 to Qt 6 because the Qt company stopped providing bug fixes for Qt 5 about a year ago. Unfortunately Qt also decided to drop support for CentOS 7. So we are currently looking into whether ChimeraX 1.3 will be the last CentOS 7 release of ChimeraX.

comment:6 by Tristan Croll, 3 years ago

I'm afraid it'll be a while yet before I have a version of ISOLDE ready for ChimeraX 1.4. The move to PyQt6 was the final push I needed to start on a long-overdue nuts-and-bolts rebuild of ISOLDE's GUI into something cleaner and more maintainable. Not something that can really be done gradually, so right now ISOLDE has a few hundred broken connections that all need to be reconnected and tested. Making good progress, but don't hold your breath.

in reply to:  7 ; comment:7 by kenneth.satyshur@…, 3 years ago 

OK. Thanks. Isolde ie great. I like the way it tweaks phi/psi so easily. I can still use the mono version with ChimeraX 1.3. Good luck with updates. It's a difficult job to maintain this so popular and necessary software. I understand that coot uses Amber for tweaks, but it tends to make the phi/psi wander outside of the allowed regions.

kas



Kenneth A. Satyshur, M.S., Ph.D.

Senior Scientist,

College of Ag and Life Sciences: Department of Bacteriology;

School of Medicine and Public Health:

Departments of Biomolecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center

(Small Molecule Screening Facility)

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, April 28, 2022 3:09 AM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Kenneth Satyshur <kenneth.satyshur@wisc.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #6692: Problem switching in/out of stereo: 'NoneType' object has no attribute 'opengl_buffer'

#6692: Problem switching in/out of stereo: 'NoneType' object has no attribute
'opengl_buffer'
---------------------------------+-------------------------
          Reporter:  satyshur@…  |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Graphics    |    Version:
        Resolution:  duplicate   |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+-------------------------

Comment (by Tristan Croll):

 I'm afraid it'll be a while yet before I have a version of ISOLDE ready
 for ChimeraX 1.4. The move to PyQt6 was the final push I needed to start
 on a long-overdue nuts-and-bolts rebuild of ISOLDE's GUI into something
 cleaner and more maintainable. Not something that can really be done
 gradually, so right now ISOLDE has a few hundred broken connections that
 all need to be reconnected and tested. Making good progress, but don't
 hold your breath.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6692#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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