Opened 4 years ago

Closed 4 years ago

#5494 closed defect (fixed)

Modeller: not enough args for format string

Reported by: chimerax-bug-report@… 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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3rc202110261847 (2021-10-26 18:47:13 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3rc202110261847 (2021-10-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> show atoms

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/subhalakshmi/Desktop/movie1.mp4

Movie saved to /Users/subhalakshmi/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/subhalakshmi/Desktop/movie2.mp4

Movie saved to /Users/subhalakshmi/Desktop/movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/subhalakshmi/Desktop/movie3.mp4

Movie saved to /Users/subhalakshmi/Desktop/movie3.mp4  
  

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

> open /Users/subhalakshmi/Documents/new_structure_pymolfiles/exp_humab.pdb

Chain information for exp_humab.pdb #1  
---  
Chain | Description  
H | No description available  
L | No description available  
  

> close

> open /Users/subhalakshmi/Documents/new_structure_pymolfiles/exp_humab.pdb
> format pdb

Chain information for exp_humab.pdb #1  
---  
Chain | Description  
H | No description available  
L | No description available  
  

> select #1

3527 atoms, 3603 bonds, 454 residues, 1 model selected  

> close

> open /Users/subhalakshmi/Downloads/exp_Vs_humab.pse

Unrecognized file suffix '.pse'  

> open /Users/subhalakshmi/Downloads/olo_expt_rank1.pdb

Summary of feedback from opening
/Users/subhalakshmi/Downloads/olo_expt_rank1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK ABodyBuilder Model of olo_expt  
  
Ignored bad PDB record found on line 2  
REMARK Model rank 1  
  
Ignored bad PDB record found on line 3  
REMARK Numbered with the imgt numbering scheme  
  
Chain information for olo_expt_rank1.pdb #1  
---  
Chain | Description  
H | No description available  
L | No description available  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/subhalakshmi/Desktop/movie4.mp4

Movie saved to /Users/subhalakshmi/Desktop/movie4.mp4  
  

> show cartoons

> lighting simple

> color bychain

Alignment identifier is 1/H  
Alignment identifier is 1/L  

> mlp

Map values for surface "olo_expt_rank1.pdb_H SES surface": minimum -29.36,
mean -5.296, maximum 22.68  
Map values for surface "olo_expt_rank1.pdb_L SES surface": minimum -28.13,
mean -6.34, maximum 21.81  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bychain

> mlp

Map values for surface "olo_expt_rank1.pdb_H SES surface": minimum -29.36,
mean -5.296, maximum 22.68  
Map values for surface "olo_expt_rank1.pdb_L SES surface": minimum -28.13,
mean -6.34, maximum 21.81  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bychain

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for olo_expt_rank1.pdb_H SES surface #1.1: minimum, -11.08,
mean -0.98, maximum 7.56  
Coulombic values for olo_expt_rank1.pdb_L SES surface #1.2: minimum, -9.63,
mean -0.65, maximum 10.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for olo_expt_rank1.pdb_H SES surface #1.1: minimum, -11.08,
mean -0.98, maximum 7.56  
Coulombic values for olo_expt_rank1.pdb_L SES surface #1.2: minimum, -9.63,
mean -0.65, maximum 10.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for olo_expt_rank1.pdb_H SES surface #1.1: minimum, -11.08,
mean -0.98, maximum 7.56  
Coulombic values for olo_expt_rank1.pdb_L SES surface #1.2: minimum, -9.63,
mean -0.65, maximum 10.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for olo_expt_rank1.pdb_H SES surface #1.1: minimum, -11.08,
mean -0.98, maximum 7.56  
Coulombic values for olo_expt_rank1.pdb_L SES surface #1.2: minimum, -9.63,
mean -0.65, maximum 10.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color bychain

[Repeated 1 time(s)]

> style stick

Changed 1762 atom styles  

> style stick

Changed 1762 atom styles  

> style sphere

Changed 1762 atom styles  

> style ball

Changed 1762 atom styles  

> color bychain

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> view

> ui tool show "Side View"

> graphics silhouettes true

> lighting flat

[Repeated 1 time(s)]

> undo

[Repeated 3 time(s)]

> view

> lighting shadows true intensity 0.5

> lighting flat

[Repeated 1 time(s)]

> lighting simple

> set bgColor white

> set bgColor black

> view orient

> view

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

[Repeated 1 time(s)]

> color bychain

> mlp

Map values for surface "olo_expt_rank1.pdb_H SES surface": minimum -29.36,
mean -5.296, maximum 22.68  
Map values for surface "olo_expt_rank1.pdb_L SES surface": minimum -28.13,
mean -6.34, maximum 21.81  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp

Map values for surface "olo_expt_rank1.pdb_H SES surface": minimum -29.36,
mean -5.296, maximum 22.68  
Map values for surface "olo_expt_rank1.pdb_L SES surface": minimum -28.13,
mean -6.34, maximum 21.81  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for olo_expt_rank1.pdb_H SES surface #1.1: minimum, -11.08,
mean -0.98, maximum 7.56  
Coulombic values for olo_expt_rank1.pdb_L SES surface #1.2: minimum, -9.63,
mean -0.65, maximum 10.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for olo_expt_rank1.pdb_H SES surface #1.1: minimum, -11.08,
mean -0.98, maximum 7.56  
Coulombic values for olo_expt_rank1.pdb_L SES surface #1.2: minimum, -9.63,
mean -0.65, maximum 10.36  
To also show corresponding color key, enter the above coulombic command and
add key true  
Destroying pre-existing alignment with identifier 1/H  
Alignment identifier is 1/H  
Destroying pre-existing alignment with identifier 1/L  
Alignment identifier is 1/L  

> interfaces ~solvent

1 buried areas: H L 769  

> interfaces ~solvent

1 buried areas: H L 769  

> show surfaces

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/subhalakshmi/Desktop/movie5.mp4

Movie saved to /Users/subhalakshmi/Desktop/movie5.mp4  
  

> lighting simple

> lighting full

> color bychain

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right select

> select /L:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /L:1-47

305 atoms, 309 bonds, 41 residues, 1 model selected  

> ui tool show "Modeller Comparative"

<QNSWindow: 0x7fe49a9a4080; contentView=<QNSView: 0x7fe486323320;
QCocoaWindow(0x600003201ad0, window=QWidgetWindow(0x60000204fa20,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  
<QNSWindow: 0x7fe49d0db870; contentView=<QNSView: 0x7fe49d2a5230;
QCocoaWindow(0x600003229fa0, window=QWidgetWindow(0x600002052d60,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  
Traceback (most recent call last):  
File
"/private/var/folders/l8/t3ttjc5538n_vjgqr1h0pnjm0000gp/T/AppTranslocation/D71EC33C-B6ED-4E95-AD63-EB3C7F86C865/d/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 201, in launch_modeller  
specific_args = "multichain %s hetPreserve %s hydrogens %s waterPreserve %s" %
(  
TypeError: not enough arguments for format string  
  
TypeError: not enough arguments for format string  
  
File
"/private/var/folders/l8/t3ttjc5538n_vjgqr1h0pnjm0000gp/T/AppTranslocation/D71EC33C-B6ED-4E95-AD63-EB3C7F86C865/d/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 201, in launch_modeller  
specific_args = "multichain %s hetPreserve %s hydrogens %s waterPreserve %s" %
(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/l8/t3ttjc5538n_vjgqr1h0pnjm0000gp/T/AppTranslocation/D71EC33C-B6ED-4E95-AD63-EB3C7F86C865/d/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 201, in launch_modeller  
specific_args = "multichain %s hetPreserve %s hydrogens %s waterPreserve %s" %
(  
TypeError: not enough arguments for format string  
  
TypeError: not enough arguments for format string  
  
File
"/private/var/folders/l8/t3ttjc5538n_vjgqr1h0pnjm0000gp/T/AppTranslocation/D71EC33C-B6ED-4E95-AD63-EB3C7F86C865/d/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/modeller/tool.py", line 201, in launch_modeller  
specific_args = "multichain %s hetPreserve %s hydrogens %s waterPreserve %s" %
(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir7,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.8 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: 8 GB
      System Firmware Version: 427.140.8.0.0
      SMC Version (system): 2.27f2

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 1 day 24 minutes

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      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

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    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: 2.1.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202110261847
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    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: 1.1.4
    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: 2.0.2
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.4
    ChimeraX-ModelPanel: 1.2
    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: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    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: 2.4.5
    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: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.0
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.21
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.1
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

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 → Modeller: not enough args for format string

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed
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