Model panel problem during movie script

[rkrishnan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
running amovie making script

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "L:\Graphics\BCRX001\GraphicsBackup\C5a complement\bcx16330f.cxc"
> format cmd

> open "L:/Graphics/BCRX001/GraphicsBackup/C5a complement/bcx16300-c5-cvf-
> complex.pdb"

Summary of feedback from opening L:/Graphics/BCRX001/GraphicsBackup/C5a
complement/bcx16300-c5-cvf-complex.pdb  
---  
warnings | Ignored bad PDB record found on line 259  
HELIX 1 1 LYS A 682 ALA A 688 1 Generated by MOE 7  
  
Ignored bad PDB record found on line 260  
HELIX 2 2 LYS A 696 TYR A 700 1 Generated by MOE 5  
  
Ignored bad PDB record found on line 261  
HELIX 3 3 PRO A 722 SER A 736 1 Generated by MOE 15  
  
Ignored bad PDB record found on line 262  
HELIX 4 4 GLN A 737 ARG A 739 5 Generated by MOE 3  
  
Ignored bad PDB record found on line 263  
HELIX 5 5 HIS A 744 HIS A 753 1 Generated by MOE 10  
  
208 messages similar to the above omitted  
  
Chain information for bcx16300-c5-cvf-complex.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> wait 150

> delete H

> split

Split bcx16300-c5-cvf-complex.pdb (#1) into 4 models  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 174, in <lambda>  
lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 214, in _fill_tree  
len_id = len(model_id)  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "new frame":  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\model_panel\tool.py", line 214, in _fill_tree  
len_id = len(model_id)  
  
See log for complete Python traceback.  
  
Chain information for bcx16300-c5-cvf-complex.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for bcx16300-c5-cvf-complex.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for bcx16300-c5-cvf-complex.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  

> split ligands

Did not split bcx16300-c5-cvf-complex.pdb A, has only one piece  
Did not split bcx16300-c5-cvf-complex.pdb B, has only one piece  
Did not split bcx16300-c5-cvf-complex.pdb C, has only one piece  
Did not split bcx16300-c5-cvf-complex.pdb E, has only one piece  

> roll x 1 90

> roll y 1 90

> wait 50

> roll Z 1 2

> roll y 1 45

> roll -x 1 10

> wait 50

> color #1.1 cornflower blue

> color #1.2 dark khaki

> color #1.3 green

> 2dlabels text "Cobra Venom Factor(CVF) " color tan size 20 xpos .7 ypos .30
> font bold

> 2dlabels text "Complement C5 alpha Chain " color cornflower blue font bold
> size 20 xpos .73 ypos .80

> 2dlabels text "Complement C5 beta Chain " color green font bold size 20 xpos
> .07 ypos .75

> wait 300

> 2dlabels #2.1 visibility false

> 2dlabels #2.3 visibility false

> view

> wait 150

> ~ribbon #1.2

> wait 50

> ~ribbon #1.3

> wait 100

> 2dlabels #2.2 visibility false

> select #1.1

6454 atoms, 6595 bonds, 2 pseudobonds, 815 residues, 2 models selected  

> view

> wait 200

> select #1.4/E:1701

31 atoms, 33 bonds, 1 residue, 1 model selected  

> hide sel

> select sel @<6 residues true

219 atoms, 212 bonds, 26 residues, 2 models selected  

> show sel

> hide #1.4/E:1701

> view

> hide cartoons

> view

> surface sel

> select #1.4/E:1701

31 atoms, 33 bonds, 1 residue, 1 model selected  

> wait 50

> select sel @<6 residues true

219 atoms, 212 bonds, 26 residues, 2 models selected  

> roll y 1 200

> roll -x 1 20

> wait 50

> surface hidePatches (#1.4#!1.1 & sel)

> color sel byhetero

> mlp sel

Map values for surface "bcx16300-c5-cvf-complex.pdb A_A SES surface": minimum
-29.48, mean -4.22, maximum 24.05  

> view

> transparency 50

> zoom 1.4

> wait 50

> turn Y 90 360 rock 180

> wait 100

> show #1.4/E:1701

> select #1.4/E:1701

31 atoms, 33 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 31 atom styles  

> select clear

> select #1.4/E:1701 @<10

429 atoms, 406 bonds, 72 residues, 3 models selected  

> hide sel

> show #1.4/E:1701

> transparency 75

> style sel ball

Changed 429 atom styles  

> wait 100

> roll y 1 90

> style sel sphere

Changed 429 atom styles  

> wait 200

> select clear

> style sel ball

Changed 0 atom styles  

> roll y 1 90

> select clear

executed bcx16330f.cxc  

> close session

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> help help:user




OpenGL version: 3.3.0 NVIDIA 452.39
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Microsoft Windows 10 Pro for Workstations (Build 19044)
Memory: 34,017,267,712
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Xeon(R) W-2145 CPU @ 3.70GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    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: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    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
    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: 1.2
    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: 1.1.1
    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: 1.5.1
    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: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    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: 1.1.0
    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: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    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: 4.10.0
    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: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    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

[Eric Pettersen]

Script to reproduce problem

[Eric Pettersen]

Thanks for reporting this problem. I have just committed a fix, and the fix will be in the next daily build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

fix: ​https://github.com/RBVI/ChimeraX/commit/2670ea429e1a93d923293d452aaa3fc1a22e26e8