chimerax.add_charge.settings missing

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-12.6.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202211090831 (2022-11-09 08:31:09 UTC)
Description
tried to use Add Charge tool

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

executed startup.cxc  
UCSF ChimeraX version: 1.6.dev202211090831 (2022-11-09)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Add Charges"

> open 1bl8 format mmcif fromDatabase pdb

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description | UniProt  
A B C D | PROTEIN (POTASSIUM CHANNEL PROTEIN) | KCSA_STRLI  
  
Non-standard residues in 1bl8 #1  
---  
K — potassium ion  
  

> ui tool show "Add Charges"

> addh #!1

Summary of feedback from adding hydrogens to 1bl8 #1  
---  
warnings | Not adding hydrogens to /A ARG 27 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A ILE 60 CG1 because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 64 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 71 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 117 NE because it is missing heavy-atom bond
partners  
15 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 117 NE; /B ARG 117 NE; /C ARG 117 NE; /D ARG 117 NE  
notes | Termini for 1bl8 (#1) chain A determined from SEQRES records  
Termini for 1bl8 (#1) chain B determined from SEQRES records  
Termini for 1bl8 (#1) chain C determined from SEQRES records  
Termini for 1bl8 (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A ALA 23, /B ALA 23, /C ALA
23, /D ALA 23  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 119, /B GLN 119, /C GLN
119, /D GLN 119  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLN 119  
Missing OXT added to C-terminal residue /B GLN 119  
Missing OXT added to C-terminal residue /C GLN 119  
Missing OXT added to C-terminal residue /D GLN 119  
340 hydrogen bonds  
2842 hydrogens added  
  
Closest equivalent command: addcharge & sel standardizeResidues
5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/tool.py", line 198, in add_h  
cb()  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 109, in <lambda>  
'callback': lambda f=self._finish_add_charge, r=residues: f(r)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 144, in _finish_add_charge  
AddNonstandardChargesTool(self.session, "Add Non-Standard Charges", non_std,  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 220, in __init__  
from .settings import get_settings  
ModuleNotFoundError: No module named 'chimerax.add_charge.settings'  
  
ModuleNotFoundError: No module named 'chimerax.add_charge.settings'  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 220, in __init__  
from .settings import get_settings  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.1 (21G217)
      Kernel Version: Darwin 21.6.0
      Time since boot: 3:20

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
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    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.43.4
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202211090831
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
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    ChimeraX-Mask: 1.0.1
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    ChimeraX-MDcrds: 2.6
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    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
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    ChimeraX-Morph: 1.0.1
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.2
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
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    ChimeraX-RemoteControl: 1.0
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    ChimeraX-RenumberResidues: 1.1
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    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
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    ChimeraX-Shell: 1.0.1
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    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
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    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
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    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
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    ihm: 0.33
    imagecodecs: 2022.7.31
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    webcolors: 1.12
    wheel: 0.37.1
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    zipp: 3.10.0

[Eric Pettersen]

Hopefully fixed in today's build, but I need to check to make sure.

[Elaine Meng]

Works fine in today's build on a couple of test cases of protein + small nonstandard ligand (4enl, 121p).

[Eric Pettersen]

Yay!