Opened 5 years ago

Closed 5 years ago

#3937 closed defect (duplicate)

Error in save error message

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 1.1 (2020-09-09 22:22:27 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: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed ChimeraX-HKCage-1.3  
Installed ChimeraX-HKCage (1.3)  

> open "C:/Users/F Mutti/WORK-Back-
> Up-2020-09-24/NEW_RESEARCH/Sheetal/Paper/Crystal
> structure/BsDyP_6KMN_template_MolA&C.pdb"

Summary of feedback from opening C:/Users/F Mutti/WORK-Back-
Up-2020-09-24/NEW_RESEARCH/Sheetal/Paper/Crystal
structure/BsDyP_6KMN_template_MolA&C.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK YASARA *************************************************************  
  
Ignored bad PDB record found on line 2  
REMARK YASARA * *  
  
Ignored bad PDB record found on line 3  
REMARK YASARA * Y A S A R A *  
  
Ignored bad PDB record found on line 4  
REMARK YASARA * *  
  
Ignored bad PDB record found on line 5  
REMARK YASARA * Yet Another Scientific Artificial Reality Application *  
  
15 messages similar to the above omitted  
  
Chain information for BsDyP_6KMN_template_MolA&C.pdb #1  
---  
Chain | Description  
A C | deferrochelatase/peroxidase efeb  
  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 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
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 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
    nucleotides tube/slab shape box

  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> set bgColor white

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> surface

> coulombic

Atoms with non-standard names found in standard residues: /C THR 313 1HG2, /C
THR 313 2HG2, /C THR 313 3HG2, /C SER 224 2HB, /C SER 224 1HB, and 3613 other
atoms. Try deleting all hydrogens first.  

> ui tool show "Show Volume Menu"

> ui tool show "Volume Viewer"

> ui tool show "Fit in Map"

> mlp

Map values for surface "BsDyP_6KMN_template_MolA&C.pdb_A SES surface": minimum
-29.23, mean -4.859, maximum 26.16  
Map values for surface "BsDyP_6KMN_template_MolA&C.pdb_C SES surface": minimum
-30.06, mean -4.907, maximum 26.91  

> coulombic

Atoms with non-standard names found in standard residues: /C THR 313 1HG2, /C
THR 313 2HG2, /C THR 313 3HG2, /C SER 224 2HB, /C SER 224 1HB, and 3613 other
atoms. Try deleting all hydrogens first.  

> surface hidePatches

> select H

5758 atoms, 748 residues, 1 model selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> coulombic

> toolshed show

> ui tool show "Show Volume Menu"

> view clip false

> view clip false

> show target m

> hide target m

> view clip false

> show target m

> ui tool show "Fit in Map"

> ui tool show "Measure and Color Blobs"

> ui tool show "Map Coordinates"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 47, in display  
self._current_option)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\manager.py", line 91, in
save_args_string_from_widget  
provider_info.format_name, self).save_args_string_from_widget(widget)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\map\\__init__.py", line 189, in save_args_string_from_widget  
return widget.options_string()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 47, in display  
self._current_option)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\manager.py", line 91, in
save_args_string_from_widget  
provider_info.format_name, self).save_args_string_from_widget(widget)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\map\\__init__.py", line 189, in save_args_string_from_widget  
return widget.options_string()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
  
See log for complete Python traceback.  
  

> save "C:/Users/F Mutti/WORK-Back-
> Up-2020-09-24/NEW_RESEARCH/Sheetal/Paper/Crystal structure/a.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 47, in display  
self._current_option)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\manager.py", line 91, in
save_args_string_from_widget  
provider_info.format_name, self).save_args_string_from_widget(widget)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\map\\__init__.py", line 189, in save_args_string_from_widget  
return widget.options_string()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
AttributeError: 'SaveModelOptionWidget' object has no attribute '_name'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\options.py", line 35, in options_string  
raise UserError("No %s to save" % self._name.lower())  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.5063
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude E7250
OS: Microsoft Windows 10 Enterprise (Build 17134)
Memory: 8,473,067,520
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-5600U CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Error in save error message

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed

Fixed on 10/5/2020

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