Phenix water placement: name 'args' is not defined

[semchonok@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)   When running Tools-->Phenix-->waterplacement, it received the error.  Is there a solution?

Thank you.

Sincrerely,

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> phenix location C:\Users\User\Phenix\phenix-installer-1.20.1-4487-intel-
> windows-x86_64\

Using Phenix installation C:\Users\User\Phenix\phenix-
installer-1.20.1-4487-intel-windows-x86_64  

> open
> D:\Projects\helix\121223__to_do__list\model_map\cropped_hepta_based_on_J1513_map.ccp4
> format ccp4

Opened cropped_hepta_based_on_J1513_map.ccp4 as #1, grid size 111,137,153,
pixel 0.765, shown at level 36.6, step 1, values float32  

> open D:/Projects/helix/121223__to_do__list/work/Afr1_2_apply_ncs_93.pdb

Summary of feedback from opening
D:/Projects/helix/121223__to_do__list/work/Afr1_2_apply_ncs_93.pdb  
---  
warnings | Ignored bad PDB record found on line 2616  
  
  
Ignored bad PDB record found on line 2662  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2608 messages similar to the above omitted  
Ignored bad PDB record found on line 5277  
  
  
Duplicate atom serial number found: 2614  
Duplicate atom serial number found: 2615  
Duplicate atom serial number found: 2616  
Duplicate atom serial number found: 2617  
Duplicate atom serial number found: 2618  
40 messages similar to the above omitted  
Ignored bad PDB record found on line 5323  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2608 messages similar to the above omitted  
Ignored bad PDB record found on line 7938  
  
  
Duplicate atom serial number found: 2614  
Duplicate atom serial number found: 2615  
Duplicate atom serial number found: 2616  
Duplicate atom serial number found: 2617  
Duplicate atom serial number found: 2618  
40 messages similar to the above omitted  
Ignored bad PDB record found on line 7984  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2608 messages similar to the above omitted  
Ignored bad PDB record found on line 10599  
  
  
Duplicate atom serial number found: 2614  
Duplicate atom serial number found: 2615  
Duplicate atom serial number found: 2616  
Duplicate atom serial number found: 2617  
Duplicate atom serial number found: 2618  
40 messages similar to the above omitted  
Ignored bad PDB record found on line 10645  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2608 messages similar to the above omitted  
Ignored bad PDB record found on line 13260  
  
  
Duplicate atom serial number found: 2614  
Duplicate atom serial number found: 2615  
Duplicate atom serial number found: 2616  
Duplicate atom serial number found: 2617  
Duplicate atom serial number found: 2618  
40 messages similar to the above omitted  
Ignored bad PDB record found on line 13306  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2608 messages similar to the above omitted  
Ignored bad PDB record found on line 15921  
  
  
Duplicate atom serial number found: 2614  
Duplicate atom serial number found: 2615  
Duplicate atom serial number found: 2616  
Duplicate atom serial number found: 2617  
Duplicate atom serial number found: 2618  
40 messages similar to the above omitted  
Ignored bad PDB record found on line 15967  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2608 messages similar to the above omitted  
Ignored bad PDB record found on line 18582  
  
  
Duplicate atom serial number found: 2614  
Duplicate atom serial number found: 2615  
Duplicate atom serial number found: 2616  
Duplicate atom serial number found: 2617  
Duplicate atom serial number found: 2618  
40 messages similar to the above omitted  
Ignored bad PDB record found on line 18628  
  
  
Ignored bad PDB record found on line 18629  
  
Chain information for Afr1_2_apply_ncs_93.pdb #2  
---  
Chain | Description  
A B C D E F G | No description available  
  

> ui tool show "Water Placement"

Traceback (most recent call last):  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 560, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1269, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\phenix_ui\\__init__.py", line 43, in start_tool  
return LaunchDouseTool(session, tool_name)  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\phenix_ui\tool.py", line 96, in __init__  
if douse_needs_resolution(session):  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\phenix_ui\douse.py", line 101, in douse_needs_resolution  
cmd = " ".join(args)  
NameError: name 'args' is not defined  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1656, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Water
Placement in bundle ChimeraX-PhenixUI:  
name 'args' is not defined  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Water
Placement in bundle ChimeraX-PhenixUI:  
name 'args' is not defined  
  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 546.33
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_150.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D95
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 34,282,192,896
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700X 8-Core Processor             
OSLanguage: pt-PT

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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-ISOLDE: 1.6.0
    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: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.1
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
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    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
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    executing: 1.2.0
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    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
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    sfftk-rw: 0.7.3
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    tzdata: 2023.3
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    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Eric Pettersen]

Reported by Dmitry Semchonok

[Eric Pettersen]

Hi Dmitry,

Thanks for reporting this problem. It is a Windows-only problem, so if you have a non-Windows system to use, you could use that for Water Placement until I can make a fix for the problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

Fixed in daily build