Opened 3 years ago

Closed 3 years ago

#7384 closed defect (fixed)

Pseudobond drawing: Cylinder end point, radii or rotation array not contiguous

Reported by: chimerax-bug-report@… 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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202208030611 (2022-08-03 06:11:58 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202208030611 (2022-08-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/pgammage/Downloads/6g2j.pdb format pdb

6g2j.pdb title:  
Mouse mitochondrial complex I In the active state [more info...]  
  
Chain information for 6g2j.pdb #1  
---  
Chain | Description | UniProt  
A | NADH dehydrogenase subunit 3 | NU3M_MOUSE  
B | nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial |
NDUS7_MOUSE  
C | nadh dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial |
NDUS3_MOUSE  
D | nadh dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial |
NDUS2_MOUSE  
E | NADH-ubiquinone oxidoreductase 24 KDA subunit | NDUV2_MOUSE  
F | nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial |
NDUV1_MOUSE  
G | nadh-ubiquinone oxidoreductase 75 kda subunit, mitochondrial | NDUS1_MOUSE  
H | NADH dehydrogenase subunit 1 | NU1M_MOUSE  
I | nadh dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial |
NDUS8_MOUSE  
J | NADH dehydrogenase subunit 6 | NU6M_MOUSE  
K | NADH dehydrogenase subunit 4L | NU4LM_MOUSE  
L | NADH dehydrogenase subunit 5 | NU5M_MOUSE  
M | NADH dehydrogenase subunit 4 | NU4M_MOUSE  
N | NADH dehydrogenase subunit 2 | NU2M_MOUSE  
O | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial |
NDUAA_MOUSE  
P | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial |
NDUA9_MOUSE  
Q | nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial |
NDUS4_MOUSE  
R | nadh dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial |
NDUS6_MOUSE  
S | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 | NDUA2_MOUSE  
T | acyl carrier protein, mitochondrial | ACPM_MOUSE  
U | acyl carrier protein, mitochondrial | ACPM_MOUSE  
V | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 | NDUA5_MOUSE  
W | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 | NDUA6_MOUSE  
X | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 | NDUA8_MOUSE  
Y | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 11 | G5E814_MOUSE  
Z | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 | NDUAD_MOUSE  
a | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 | NDUA1_MOUSE  
b | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 3 | NDUA3_MOUSE  
c | nadh dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | NDUC1_MOUSE  
d | nadh dehydrogenase [ubiquinone] 1 subunit C2 | NDUC2_MOUSE  
e | nadh dehydrogenase [ubiquinone] iron-sulfur protein 5 | NDUS5_MOUSE  
f | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 1 | NDUB1_MOUSE  
g | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial |
NDUBB_MOUSE  
h | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial |
NDUB5_MOUSE  
i | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 6 | NDUB6_MOUSE  
j | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial |
NDUB2_MOUSE  
k | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 3 | NDUB3_MOUSE  
l | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial |
NDUB8_MOUSE  
m | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 4 | NDUB4_MOUSE  
n | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 9 | NDUB9_MOUSE  
o | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 7 | NDUB7_MOUSE  
p | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 | NDUBA_MOUSE  
q | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 | NDUAC_MOUSE  
r | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 7 | NDUA7_MOUSE  
s | nadh dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial |
NDUV3_MOUSE  
  
Non-standard residues in 6g2j.pdb #1  
---  
2MR — N3, N4-dimethylarginine  
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)  
ADP — adenosine-5'-diphosphate  
AME — N-acetylmethionine  
AYA — N-acetylalanine  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
EHZ — ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-
butanoyl]amino]propanoylamino]ethyl](3~{S})-3-oxidanyltetradecanethioate  
FES — FE2/S2 (inorganic) cluster  
FME — N-formylmethionine  
FMN — flavin mononucleotide (riboflavin monophosphate)  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotidephosphate  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
SAC — N-acetyl-serine  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> select
> ::name="2MR"::name="3PE"::name="ADP"::name="AME"::name="AYA"::name="CDL"::name="EHZ"::name="FES"::name="FME"::name="FMN"::name="NDP"::name="PC1"::name="SAC"::name="SF4"::name="ZN"

1354 atoms, 1351 bonds, 46 residues, 1 model selected  

> hide sel target a

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1766, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 358, in update_graphics_if_needed  
self._update_graphics(gc)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 376, in _update_graphics  
pbg._update_graphics(changes)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 221, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 238, in _update_positions  
return s._halfbond_cylinder_placements(axyz0, axyz1, pbonds.radii)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2284, in
_halfbond_cylinder_placements  
half_cylinder_rotations(axyz0, axyz1, radii, p)  
ValueError: Cylinder end point, radii or rotation array not contiguous.  
  
Error processing trigger "graphics update":  
ValueError: Cylinder end point, radii or rotation array not contiguous.  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 2284, in
_halfbond_cylinder_placements  
half_cylinder_rotations(axyz0, axyz1, radii, p)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.4.5
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 90 days 2:36

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.5
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.7.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.0
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.5.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.7
    ChimeraX-AtomicLibrary: 7.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1.1
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.1
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202208030611
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.6
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.2.1
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.5
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.21.4
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.2
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 0.9.1
    filelock: 3.4.2
    fonttools: 4.34.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.4.0
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.3
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.12.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.30
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.2.0
    qtconsole: 5.3.1
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 62.6.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.3.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.11
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.3.0
    zipp: 3.8.1

Change History (4)

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 → Pseudobond drawing: Cylinder end point, radii or rotation array not contiguous

comment:2 by Tom Goddard, 3 years ago

This reproduces for me in the daily build using the 3 commands in the log of the bug report.

comment:3 by Tom Goddard, 3 years ago

Numpy 1.23 introduced this bug with the following change

​https://github.com/numpy/numpy/pull/21477

that makes the strides of a 0 length array all 0. In this ChimeraX bug a zero length array of atom coordinates which had strides (24,8) in numpy 1.22 now has strides (0,0) and our C++ array checking code decides it is therefore not contiguous.

comment:4 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Changed the arrays C++ code is_contiguous() method to accept 0 length arrays as contiguous no matter what the strides are.

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