Opened 4 years ago

Closed 4 years ago

#6172 closed defect (duplicate)

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

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

Description 

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
camera stereo while in isolde.

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  

> open 2bbv format mmcif fromDatabase pdb

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description | UniProt  
A B C | protein (black beetle virus capsid protein) | COAT_BBV  
D E F | protein (black beetle virus capsid protein) | COAT_BBV  
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |  
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> camera stereo

> camera mono

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 32 residues in model #1 to IUPAC-IUB
standards.  
2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C | protein (black beetle virus capsid protein) | COAT_BBV  
1.2/D 1.2/E 1.2/F | protein (black beetle virus capsid protein) | COAT_BBV  
1.2/N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |  
  
Non-standard residues in 2bbv #1.2  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to 2bbv #1.2  
---  
warnings | Not adding hydrogens to /A SER 336 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /B SER 336 CB because it is missing heavy-atom bond
partners  
notes | Termini for 2bbv (#1.2) chain N determined from SEQRES records  
Termini for 2bbv (#1.2) chain A determined from SEQRES records  
Termini for 2bbv (#1.2) chain D determined from SEQRES records  
Termini for 2bbv (#1.2) chain B determined from SEQRES records  
Termini for 2bbv (#1.2) chain E determined from SEQRES records  
2 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /D ALA 364, /E ALA 364, /F
ALA 364  
Chain-initial residues that are not actual N termini: /A LEU 56, /B LEU 56, /C
THR 20, /C ALA 55  
Chain-final residues that are actual C termini: /A ASN 363, /B ASN 363, /C ASN
363  
Chain-final residues that are not actual C termini: /D ALA 379, /E ALA 379, /C
PRO 31, /F ALA 379  
973 hydrogen bonds  
Adding 'H' to /A LEU 56  
Adding 'H' to /B LEU 56  
Adding 'H' to /C THR 20  
Adding 'H' to /C ALA 55  
/D ALA 379 is not terminus, removing H atom from 'C'  
/E ALA 379 is not terminus, removing H atom from 'C'  
/F ALA 379 is not terminus, removing H atom from 'C'  
7821 hydrogens added  
  

> open 20205 fromDatabase emdb

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  

> 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  
/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py:2021: RuntimeWarning: divide by zero
encountered in double_scalars  
self.global_k = scaling_constant/ref_g  

> open 20205 fromDatabase emdb

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  

> clipper associate #2 toModel #1

Opened emdb 20205 as #1.1.1.2, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at step 1, values float32  

> close #1.1

> close #1.3

> close #1.1

[Repeated 1 time(s)]

> close #1

> 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  
  
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 | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

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  

> 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  

> camera stereo

> hide HC

> 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  
  

> 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  
1205 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'  
0 hydrogens added  
  

> isolde restrain ligands #1

> hide HC

> select #1

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

> camera mono

> cview /A:57

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

> 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        3.7G        390M         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

Change History (3)

in reply to:  1 ; comment:1 by kenneth.satyshur@…, 4 years ago 

graphics restart causes a crash

(chimerax:12680): dbind-WARNING **: 14:40:47.238: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-8UnesD0Wzq: Connection refused
Missing dihedral chi1 for residue A336: SER
Missing dihedral chi1 for residue B336: SER
Missing dihedral chi1 for residue A336: SER
Missing dihedral chi1 for residue B336: SER
Gtk-Message: 14:45:28.633: GtkDialog mapped without a transient parent. This is discouraged.

(chimerax:12680): IBUS-WARNING **: 14:45:28.639: Unable to connect to ibus: Could not connect: Connection refused
Gtk-Message: 14:45:32.261: GtkDialog mapped without a transient parent. This is discouraged.
Segmentation fault (core dumped)
[satyshur@kenworkathome ~/isolde]$


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: Tuesday, February 15, 2022 3:03 PM
To: Kenneth Satyshur <kenneth.satyshur@wisc.edu>
Subject: [ChimeraX] #6172: ChimeraX bug report submission

#6172: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  satyshur@…  |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
 {{{
 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
 camera stereo while in isolde.

 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

 > open 2bbv format mmcif fromDatabase pdb

 2bbv title:
 The refined three-dimensional structure of an insect virus At 2.8
 angstroms
 resolution [more info...]

 Chain information for 2bbv #1
 ---
 Chain | Description | UniProt
 A B C | protein (black beetle virus capsid protein) | COAT_BBV
 D E F | protein (black beetle virus capsid protein) | COAT_BBV
 N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |

 Non-standard residues in 2bbv #1
 ---
 CA — calcium ion

 2bbv mmCIF Assemblies
 ---
 1| complete icosahedral assembly
 2| icosahedral asymmetric unit
 3| icosahedral pentamer
 4| icosahedral 23 hexamer
 5| icosahedral asymmetric unit, std point frame
 6| crystal asymmetric unit, crystal frame


 > camera stereo

 > camera mono

 > ui tool show ISOLDE

 > set selectionWidth 4

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 32 residues in model #1 to IUPAC-
 IUB
 standards.
 2bbv title:
 The refined three-dimensional structure of an insect virus At 2.8
 angstroms
 resolution [more info...]

 Chain information for 2bbv
 ---
 Chain | Description | UniProt
 1.2/A 1.2/B 1.2/C | protein (black beetle virus capsid protein) | COAT_BBV
 1.2/D 1.2/E 1.2/F | protein (black beetle virus capsid protein) | COAT_BBV
 1.2/N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |

 Non-standard residues in 2bbv #1.2
 ---
 CA — calcium ion

 2bbv mmCIF Assemblies
 ---
 1| complete icosahedral assembly
 2| icosahedral asymmetric unit
 3| icosahedral pentamer
 4| icosahedral 23 hexamer
 5| icosahedral asymmetric unit, std point frame
 6| crystal asymmetric unit, crystal frame

 Done loading forcefield

 > addh

 Summary of feedback from adding hydrogens to 2bbv #1.2
 ---
 warnings | Not adding hydrogens to /A SER 336 CB because it is missing
 heavy-
 atom bond partners
 Not adding hydrogens to /B SER 336 CB because it is missing heavy-atom
 bond
 partners
 notes | Termini for 2bbv (#1.2) chain N determined from SEQRES records
 Termini for 2bbv (#1.2) chain A determined from SEQRES records
 Termini for 2bbv (#1.2) chain D determined from SEQRES records
 Termini for 2bbv (#1.2) chain B determined from SEQRES records
 Termini for 2bbv (#1.2) chain E determined from SEQRES records
 2 messages similar to the above omitted
 Chain-initial residues that are actual N termini: /D ALA 364, /E ALA 364,
 /F
 ALA 364
 Chain-initial residues that are not actual N termini: /A LEU 56, /B LEU
 56, /C
 THR 20, /C ALA 55
 Chain-final residues that are actual C termini: /A ASN 363, /B ASN 363, /C
 ASN
 363
 Chain-final residues that are not actual C termini: /D ALA 379, /E ALA
 379, /C
 PRO 31, /F ALA 379
 973 hydrogen bonds
 Adding 'H' to /A LEU 56
 Adding 'H' to /B LEU 56
 Adding 'H' to /C THR 20
 Adding 'H' to /C ALA 55
 /D ALA 379 is not terminus, removing H atom from 'C'
 /E ALA 379 is not terminus, removing H atom from 'C'
 /F ALA 379 is not terminus, removing H atom from 'C'
 7821 hydrogens added


 > open 20205 fromDatabase emdb

 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

 > 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
 /home/satyshur/.local/share/ChimeraX/1.3/site-
 packages/chimerax/isolde/molobject.py:2021: RuntimeWarning: divide by zero
 encountered in double_scalars
 self.global_k = scaling_constant/ref_g

 > open 20205 fromDatabase emdb

 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

 > clipper associate #2 toModel #1

 Opened emdb 20205 as #1.1.1.2, grid size 98,112,104, pixel 1.07,1.07,1.07,
 shown at step 1, values float32

 > close #1.1

 > close #1.3

 > close #1.1

 [Repeated 1 time(s)]

 > close #1

 > 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

 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 | capsid protein VP1 | CAPSD_NVN68
 1.2/B | capsid protein VP1 | CAPSD_NVN68
 1.2/C | capsid protein VP1 | CAPSD_NVN68

 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205

 > open 20205 fromDatabase emdb

 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

 > 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

 > camera stereo

 > hide HC

 > 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


 > 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
 1205 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'
 0 hydrogens added


 > isolde restrain ligands #1

 > hide HC

 > select #1

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

 > camera mono

 > cview /A:57

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

 > 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        3.7G        390M
 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

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6172>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 4 years ago

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

comment:3 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: assigned → closed
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