KVFinder "nearby" value not valid

[thibault.tubiana@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9rc202411230619 (2024-11-23 06:19:23 UTC)
Description
"Nearby" atom/residue distance not valid with cavities (kvfinder). 

In the cavities windows, The default value of 3.5A give the following error : "Nearby" atom/residue distance not valid.  I can change it to integer values, but not float (comma or "." doesn't work). 
My windows is french... Maybe it is linked ? 

Best regards,
Thibault.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2H4G format mmcif fromDatabase pdb

2h4g title:  
Crystal structure of PTP1B with monocyclic thiophene inhibitor [more info...]  
  
Chain information for 2h4g #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein phosphatase non-receptor type 1 | PTN1_HUMAN 1-299  
  
Non-standard residues in 2h4g #1  
---  
694 — 4-bromo-3-(carboxymethoxy)-5-(4-hydroxyphenyl)thiophene-2-carboxylic
acid  
  
Drag select of 1 atoms  

> select add /A:304@O

2 atoms, 1 bond, 2 residues, 1 model selected  

> select up

4 atoms, 1 bond, 3 residues, 1 model selected  

> select up

23 atoms, 22 bonds, 3 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

pyKVFinder module not installed; fetching from PyPi repository...  

> kvfinder #1

14 cavities found for 2h4g #1  
2h4g Cavities  
---  
ID |  | Volume | Area | Points  
1.1.6 |  | 134.78 | 113.59 | 624  
1.1.2 |  | 60.91 | 83.25 | 282  
1.1.5 |  | 48.6 | 56.48 | 225  
1.1.13 |  | 26.35 | 39.62 | 122  
1.1.8 |  | 24.62 | 46.53 | 114  
1.1.7 |  | 22.25 | 35.72 | 103  
1.1.11 |  | 21.38 | 35.91 | 99  
1.1.4 |  | 19.87 | 36.19 | 92  
1.1.1 |  | 16.85 | 39.15 | 78  
1.1.3 |  | 15.98 | 23.87 | 74  
1.1.9 |  | 11.23 | 21.14 | 52  
1.1.12 |  | 9.07 | 20.7 | 42  
1.1.14 |  | 6.7 | 13.93 | 31  
1.1.10 |  | 5.18 | 10.99 | 24  
  

> view #1.1.6 @< 3.5

> zoom 0.75

moved plane near -26.14409739588395 [-0.74789216 0.16373095 0.64331135]  
moved plane far -26.14409739588395 [-0.74789216 0.16373095 0.64331135]  

> surface #1.1

> transparency #1.1 50

> ~surface #1.1

> surface #1.1.6

"Nearby" atom/residue distance not valid  

> view #!1.1.2 @< 3.5

> zoom 0.75

moved plane near -23.322415246558013 [0.26635626 0.44317941 0.85594763]  
moved plane far -23.322415246558013 [0.26635626 0.44317941 0.85594763]  

> ~surface #1.1

> surface #!1.1.2

"Nearby" atom/residue distance not valid  

> view #!1.1.6 @< 3.5

> zoom 0.75

moved plane near -28.718391759469373 [ 0.60252069 -0.53292798 0.5941015 ]  
moved plane far -28.718391759469373 [ 0.60252069 -0.53292798 0.5941015 ]  

> ~surface #1.1

> surface #!1.1.6

> show #!1 & (#!1.1.6 :< 5.0)

> view #!1.1.2 @< 5.0

> zoom 0.75

moved plane near -28.386186115314302 [ 0.60252069 -0.53292798 0.5941015 ]  
moved plane far -28.386186115314302 [ 0.60252069 -0.53292798 0.5941015 ]  

> ~surface #1.1

> surface #!1.1.2

> show #!1 & (#!1.1.2 :< 5.0)




OpenGL version: 3.3.0 NVIDIA 560.76
OpenGL renderer: NVIDIA RTX 3000 Ada Generation Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: fr_FR.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision 5480
OS: Microsoft Windows 11 Professionnel (Build 22631)
Memory: 68,307,476,480
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i9-13900H
OSLanguage: fr-FR

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
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    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411230619
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
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    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
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    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.3.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
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    comm: 0.2.2
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    ipykernel: 6.29.5
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[Eric Pettersen]

Hi Thibault,

Thanks for reporting this problem. I'm guessing it must be related to your French localization on your Windows machine, since it works fine for me. To try that out I'm going to have to wait until I'm in the office next week and have access to a Windows machine that I can change the localization for.
In the interim, I'm hoping you could try a couple of tests for me. One would be to bring up the Build Structure tool, choose to add a peptide, input any sequence (e.g. "AAA", click Apply, and in the resulting dialog change the phi or psi values (or both) to non-integer numbers and then click the "Set" button. Does that work or do you get an error?
The other test is to temporarily change your machine to English localization (if possible) and see if Find Cavities then works.
Thanks for any info you can provide.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[thibault.tubiana@…]

Hi Eric!

Thank you for your response, it's not a urgent bug but I just wanted to report it :) 
In the build structure I cannot put "." to have float, but I can put a comma, however it does not convert it to float afterwards (ValueError: could not convert string to float: '-57,5')

Best regards,
Thibault Tubiana.

----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: pett@cgl.ucsf.edu, "Thibault TUBIANA" <thibault.tubiana@i2bc.paris-saclay.fr>
Envoyé: Mardi 26 Novembre 2024 20:38:10
Objet: Re: [ChimeraX] #16374: KVFinder "nearby" value not valid

#16374: KVFinder "nearby" value not valid
-----------------------------------------------+----------------------
          Reporter:  thibault.tubiana@\u2026        |      Owner:  pett
              Type:  defect                    |     Status:  feedback
          Priority:  normal                    |  Milestone:
         Component:  Surface/Binding Analysis  |    Version:
        Resolution:                            |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback

Comment:

 Hi Thibault,
         Thanks for reporting this problem.  I'm guessing it must be
 related to your French localization on your Windows machine, since it
 works fine for me.  To try that out I'm going to have to wait until I'm in
 the office next week and have access to a Windows machine that I can
 change the localization for.
         In the interim, I'm hoping you could try a couple of tests for me.
 One would be to bring up the Build Structure tool, choose to add a
 peptide, input any sequence (e.g. "AAA", click Apply, and in the resulting
 dialog change the phi or psi values (or both) to non-integer numbers and
 then click the "Set" button.  Does that work or do you get an error?
         The other test is to temporarily change your machine to English
 localization (if possible) and see if Find Cavities then works.
         Thanks for any info you can provide.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

[Eric Pettersen]

Hi Thibault,

This is fixed in the daily build now. Since the fix required changing a global Qt setting (about interpreting number strings), we weren't comfortable putting it in the release candidate at this late point in the release cycle -- we want to see if there are any other ramifications to other parts of the code due to the change. So you will have to use the daily build if you want to change that Find Cavities parameter.

--Eric