Opened 4 years ago

Closed 4 years ago

#6608 closed defect (duplicate)

Can't show sequence

Reported by: uzay.sezen@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.4.dev202204130407 (2022-04-13 04:07:52 UTC)
Description
I morphed two pdb structures. Sequence viewer fails to show sequence of the morphed coordinate set.

Log:
UCSF ChimeraX version: 1.4.dev202204130407 (2022-04-13)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/WhitePines/Pila-Pita/TFIIF/AlphaFold/prediction_PilaTFIIFab-
> dimer/PilaChainATFIIFb.pdb

Summary of feedback from opening C:/WhitePines/Pila-
Pita/TFIIF/AlphaFold/prediction_PilaTFIIFab-dimer/PilaChainATFIIFb.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 12 12 ASP B
70 TYR B 76 1 7  
Start residue of secondary structure not found: HELIX 13 13 LEU B 136 ASN B
163 1 28  
Start residue of secondary structure not found: HELIX 14 14 GLY B 164 ALA B
167 1 4  
Start residue of secondary structure not found: HELIX 15 15 GLY B 169 GLY B
176 1 8  
Start residue of secondary structure not found: HELIX 16 16 GLU B 213 ARG B
224 1 12  
17 messages similar to the above omitted  
  
Chain information for PilaChainATFIIFb.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open C:/WhitePines/Pila-Pita/TFIIF/pila-eugr-TFIIFb-sm.pdb

pila-eugr-TFIIFb-sm.pdb title:  
SWISS-MODEL SERVER (http://swissmodel.expasy.org) pilaTFIIFb-eugr [more
info...]  
  
Chain information for pila-eugr-TFIIFb-sm.pdb #2  
---  
Chain | Description  
A | No description available  
  

> matchmaker #2 to #1

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 PilaChainATFIIFb.pdb, chain A (#1) with pila-eugr-TFIIFb-sm.pdb,
chain A (#2), sequence alignment score = 1176.1  
RMSD between 45 pruned atom pairs is 0.812 angstroms; (across all 288 pairs:
39.045)  
  

> morph #2,1

Computed 51 frame morph #3  

> coordset #3 1,51

> show #1 models

> show #2 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\show_sequences\tool.py", line 64, in show_seqs  
run(self.session, "seq chain %s" % " ".join([chain.atomspec for chain in
chains]))  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 211, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 243, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 99, in __init__  
self.associate(None, keep_intrinsic=True)  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 186, in associate  
self.associate([], seq=seq, reassoc=reassoc, keep_intrinsic=keep_intrinsic)  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 205, in associate  
self.prematched_assoc_structure(match_map, 0, reassoc)  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
AttributeError: 'Chain' object has no attribute 'match_maps'  
  
AttributeError: 'Chain' object has no attribute 'match_maps'  
  
File "C:\Program Files\ChimeraX 1.4.dev202204130407\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 576, in
prematched_assoc_structure  
aseq.match_maps[chain] = match_map  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 391.35
OpenGL renderer: GeForce GTX 580/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt runtime version: 6.2.4
Qt platform: windows

Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 17,133,236,224
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    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: 2.4.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.37.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.2
    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: 2.2.3
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202204130407
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.4
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.0.1
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.32.0
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.8
    PyQt6-commercial: 6.2.3
    PyQt6-Qt6: 6.2.4
    PyQt6-sip: 13.2.1
    PyQt6-WebEngine-commercial: 6.2.1
    PyQt6-WebEngine-Qt6: 6.2.4
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Can't show sequence

comment:2 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Uzay,

Thanks for reporting this problem. It was only that one daily build that you have, so if you just get the current daily build you won't run into it again. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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