Opened 2 years ago

Closed 2 years ago

#9357 closed defect (fixed)

Coloring AlphaFold PAE domains: IndexError: index 907 is out of bounds for axis 0 with size 907

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

Description 

The following bug report has been submitted:
Platform:        macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.7.dev202307092334 (2023-07-09 23:34:17 UTC)
Description
After deleting part of alphafold prediction and pressing pae plot Color PAE Domains button I got this error.  I had used this button before I deleted some chains of the structure.

Log:
Startup Messages  
---  
notes | 2023-07-11 11:39:07,476:INFO:OpenGL_accelerate module loaded  
2023-07-11 11:39:07,482:INFO:Using accelerated ArrayDatatype  
  
UCSF ChimeraX version: 1.7.dev202307092334 (2023-07-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8guy

8guy title:  
human insulin receptor bound with two insulin molecules [more info...]  
  
Chain information for 8guy #1  
---  
Chain | Description | UniProt  
A C | Insulin A chain | INS_HUMAN 1-21  
B D | Insulin, isoform 2 | INSR2_HUMAN 3-27  
E F | Isoform Short of Insulin receptor | INSR_HUMAN 1-907  
  

> close

> open /Users/goddard/ucsf/presentations/chimerax-paper-
> jul2023/alphafold/insr_ins_human_dimer/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  

> color /A-D orange

> color /E tan

> color /F cornflowerblue

> set bgColor white

> graphics silhouettes true

> save /Users/goddard/Desktop/image1.png supersample 3

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file /Users/goddard/ucsf/presentations/chimerax-paper-
> jul2023/alphafold/insr_ins_human_dimer/best_model_pae.json

> color bfactor #1 palette alphafold

15262 atoms, 1906 residues, atom bfactor range 15.5 to 97  

> save /Users/goddard/Desktop/image1.png supersample 3

> alphafold pae #1 colorDomains true

> save /Users/goddard/Desktop/image1.png supersample 3

> open /Users/goddard/ucsf/presentations/chimerax-paper-
> jul2023/alphafold/insr_ins_human_dimer/af1906_unrelaxed_rank_00[2-5]*.pdb

Chain information for
af1906_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb #2  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  
Chain information for
af1906_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb #3  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  
Chain information for
af1906_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb #4  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  
Chain information for
af1906_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb #5  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  

> mmaker #2-5/E to #1/E

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain E (#1) with
af1906_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_000.pdb, chain E
(#2), sequence alignment score = 4713.7  
RMSD between 340 pruned atom pairs is 0.969 angstroms; (across all 907 pairs:
14.449)  
  
Matchmaker best_model.pdb, chain E (#1) with
af1906_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb, chain E
(#3), sequence alignment score = 4720.9  
RMSD between 440 pruned atom pairs is 1.239 angstroms; (across all 907 pairs:
4.202)  
  
Matchmaker best_model.pdb, chain E (#1) with
af1906_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb, chain E
(#4), sequence alignment score = 4703.5  
RMSD between 349 pruned atom pairs is 0.921 angstroms; (across all 907 pairs:
15.834)  
  
Matchmaker best_model.pdb, chain E (#1) with
af1906_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb, chain E
(#5), sequence alignment score = 4733.5  
RMSD between 346 pruned atom pairs is 0.990 angstroms; (across all 907 pairs:
16.613)  
  

> hide /F

> color /A-D orange

> hide atoms

> show cartoons

> hide /F cartoons

> hide /A,B cartoons

> show /A,B cartoons

> hide :716-757 cartoons

> rainbow #1-5 structures

> color /A-D orange

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 76310 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> hide /F ribbons

> hide :716-757 cartoons

> surface #1-5/A-E

> surface close

> show atoms

> show cartoons

> hide cartoons

> style sphere

Changed 76310 atom styles  

> hide /F

> hide :716-757 cartoons

> hide :716-757

> show cartoons

> hide atoms

> hide :716-757

> hide :716-757 ribbons

> hide /F ribbons

> rainbow #1-5 structures palette redblue

> rainbow #1-5 structures palette gray

> rainbow #1-5 structures palette cyan-gray-maroon

> rainbow #1-5 structures palette paegreen

Fetching compressed palette Set5 from
http://www.colourlovers.com/api/palettes?keywords=Set5&format=json&numResults=100  
Could not find palette Set5 at COLOURlovers.com using keyword search  

> rainbow #1-5 structures palette oranges

> rainbow #1-5 structures palette blues

> hide /A-D ribbons

> surface /A-D

> color /A-D orange

> save /Users/goddard/Desktop/image1.png supersample 3

> save /Users/goddard/ucsf/presentations/chimerax-paper-
> jul2023/images/af1906_aligned.cxs

> close

> open /Users/goddard/ucsf/presentations/chimerax-paper-
> jul2023/alphafold/insr_ins_human_dimer/best_model.pdb format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file /Users/goddard/ucsf/presentations/chimerax-paper-
> jul2023/alphafold/insr_ins_human_dimer/best_model_pae.json

> alphafold pae #1 colorDomains true

> select /A-D

724 atoms, 736 bonds, 92 residues, 1 model selected  

> delete ~/B,C,E

> select clear

> color bfactor #1 palette alphafold

7631 atoms, 953 residues, atom bfactor range 15.5 to 97  

> hide atoms

> show cartoons

> delete /B,C

> alphafold pae #1 colorDomains true

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 545, in _color_domains  
self._pae.color_domains(log_command = True)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 914, in color_domains  
color_by_pae_domain(m.residues, self._clusters, colors=self._cluster_colors)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1126, in color_by_pae_domain  
cresidues = residues[array(list(c),int32)]  
~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molarray.py", line 158, in __getitem__  
v = self.__class__(self._pointers[i])  
~~~~~~~~~~~~~~^^^  
IndexError: index 907 is out of bounds for axis 0 with size 907  
  
IndexError: index 907 is out of bounds for axis 0 with size 907  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molarray.py", line 158, in __getitem__  
v = self.__class__(self._pointers[i])  
~~~~~~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (22E261)
      Kernel Version: Darwin 22.4.0
      Time since boot: 63 days, 1 hour, 24 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46
    ChimeraX-AtomicLibrary: 10.0.7
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307092334
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    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: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.30.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.40.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.3.16
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.8.1
    prompt-toolkit: 3.0.39
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.1.0
    pyproject-hooks: 1.0.0
    PyQt6: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8

Change History (2)

comment:1 by Tom Goddard, 2 years ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Coloring AlphaFold PAE domains: IndexError: index 907 is out of bounds for axis 0 with size 907

comment:2 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Added a clear error message that PAE domains cannot be colored if parts of structure is deleted.

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