Opened 3 years ago

Closed 3 years ago

#7695 closed defect (fixed)

Bug in matchmaker secondary structure code revamp

Reported by: lindseycalva@… Owned by: Eric Pettersen
Priority: high Milestone:
Component: Structure Comparison Version:
Keywords: Cc: Elaine Meng
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.dev202209232318 (2022-09-23 23:18:29 UTC)
Description
(Describe the actions that caused this problem to occur here) I am trying to morph two different chains and it is not working when I do that. I can conduct the matchmaker comand without issue and then the morph just says aligning 1 of 1 then nothing happens and I get an error box that pops up.

Log:
UCSF ChimeraX version: 1.5.dev202209232318 (2022-09-23)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/lindseycalva/Downloads/5o2k.pdb format pdb

5o2k.pdb title:  
Native apo-structure of pseudomonas stutzeri PTXB to 2.1 A resolution [more
info...]  
  
Chain information for 5o2k.pdb #1  
---  
Chain | Description | UniProt  
A | probable phosphite transport system-binding protein PTXB | PTXB_PSEST  
B | probable phosphite transport system-binding protein PTXB | PTXB_PSEST  
C D | probable phosphite transport system-binding protein PTXB | PTXB_PSEST  
E | probable phosphite transport system-binding protein PTXB | PTXB_PSEST  
F | probable phosphite transport system-binding protein PTXB | PTXB_PSEST  
  

> set bgColor white

> open /Users/lindseycalva/Downloads/5o2j.pdb

5o2j.pdb title:  
Pseudomonas stutzeri PTXB In complex with phosphite to 1.52 A resolution [more
info...]  
  
Chain information for 5o2j.pdb #2  
---  
Chain | Description | UniProt  
A | probable phosphite transport system-binding protein PTXB | PTXB_PSEST  
  
Non-standard residues in 5o2j.pdb #2  
---  
2PO — phosphonate  
EDO — 1,2-ethanediol (ethylene glycol)  
  

> select #1/E

2054 atoms, 2035 bonds, 317 residues, 1 model selected  

> delete #1/E

> delete #1/D

> delete #1/C

> delete #1/B

> delete #1/A

> select #1/F

2029 atoms, 2019 bonds, 305 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> matchmaker #1 to 2

Invalid "to" argument: invalid atoms specifier  

> matchmaker #1 to #2

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 5o2j.pdb, chain A (#2) with 5o2k.pdb, chain F (#1), sequence
alignment score = 1234.9  
RMSD between 81 pruned atom pairs is 0.354 angstroms; (across all 252 pairs:
12.207)  
  

> morph #1,2

Traceback (most recent call last):  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/motion.py", line 111, in segment_and_pair_atoms  
results = segmentHingeExact(sm, m, cf, mhs, log=log)  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/segment.py", line 109, in segmentHingeExact  
raise AtomPairingError('%s chain %s (%d) and %s chain %s (%d) have different
number of residues'  
chimerax.morph.segment.AtomPairingError: Morph - 5o2k.pdb chain F (305) and
5o2j.pdb chain A (454) have different number of residues  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/motion.py", line 24, in compute_morph  
res_groups, atom_map, trimmed = motion.segment_and_pair_atoms(mol)  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/motion.py", line 114, in segment_and_pair_atoms  
results = segmentHingeApproximate(sm, m, cf, mhs, log=log)  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/morph/segment.py", line 190, in segmentHingeApproximate  
score, gapped0, gapped1 = align(session, seq0, seq1,  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
AttributeError: 'set' object has no attribute 'items'  
  
AttributeError: 'set' object has no attribute 'items'  
  
File
"/private/var/folders/0x/8x8fm08d75g5hwvqsc18bz7r0000gn/T/AppTranslocation/779224BC-E73D-46FA-A0B2-451170895D1A/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 181, in align  
for s, ss_info in dssp_cache.items():  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.7
OpenGL renderer: Intel HD Graphics 5000 OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir6,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 4 GB
      System Firmware Version: 432.60.3.0.0
      SMC Version (system): 2.13f15

Software:

    System Software Overview:

      System Version: macOS 11.6.2 (20G314)
      Kernel Version: Darwin 20.6.0
      Time since boot: 6 days 7:44

Graphics/Displays:

    Intel HD Graphics 5000:

      Chipset Model: Intel HD Graphics 5000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a26
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          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: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.3
    ChimeraX-AtomicLibrary: 8.0.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.2
    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.dev202209232318
    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: 1.3
    ChimeraX-DockPrep: 1.0
    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: 2.4
    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-Label: 1.1.7
    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: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    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: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    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: 1.24.1
    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: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.0
    filelock: 3.7.1
    fonttools: 4.37.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.3
    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: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    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: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    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: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    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: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1
File attachment: 5o2k.pdb

5o2k.pdb​

Attachments (1)

5o2k.pdb​ (1.0 MB ) - added by lindseycalva@… 3 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

by lindseycalva@…, 3 years ago

Attachment: 5o2k.pdb​ added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Bug in matchmaker secondary structure code revamp

comment:2 by Eric Pettersen, 3 years ago

Priority: normal → high

comment:3 by Eric Pettersen, 3 years ago

Cc: Elaine Meng added

comment:4 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: accepted → closed

Fix will be in tomorrow's daily build.

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