Clicking "Coloring" in AlphaFold panel does not show the coloring panel

[yen-li.li@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202109060834 (2021-09-06 08:34:57 UTC)
Description
When I click "Coloring" in AlphaFold panel, the coloring panel didn't show up. 

Log:
UCSF ChimeraX version: 1.3.dev202109060834 (2021-09-06)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6p59 format mmcif fromDatabase pdb

6p59 title:  
Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex [more info...]  
  
Chain information for 6p59 #1  
---  
Chain | Description | UniProt  
A C | Core-binding factor subunit β | PEBB_HUMAN  
B F | Virion infectivity factor | E1ANT9_SIV  
D W | Elongin-B | ELOB_HUMAN  
E Z | Elongin-C | ELOC_HUMAN  
  
Non-standard residues in 6p59 #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MES — 2-(N-morpholino)-ethanesulfonic acid  
ZN — zinc ion  
  
6p59 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> show atoms

> hide atoms

> show cartoons

> delete #1/C,F,W,Z

> ui tool show AlphaFold

> alphafold match #1/E

1 AlphaFold model found using UniProt identifier: Q15369 (chain E)  
AlphaFold chains matching 6p59  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
E | ELOC_HUMAN | Q15369 | 2.36 | 112 | 96 | 100  
  
Opened 1 AlphaFold model  

> help help:user/tools/alphafold.html




OpenGL version: 3.3.0 NVIDIA 471.68
OpenGL renderer: NVIDIA GeForce RTX 2060 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 34,261,569,536
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('zh_TW', 'cp950')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    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: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109060834
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 2.1.1
    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
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    ChimeraX-MDcrds: 2.5
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    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
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    ChimeraX-OpenCommand: 1.7
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    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: 2.4.3
    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
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    ChimeraX-UnitCell: 1.0
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    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
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    ChimeraX-WebCam: 1.0
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    ChimeraX-Zone: 1.0
    colorama: 0.4.4
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    cycler: 0.10.0
    Cython: 0.29.23
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    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
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File attachment: AlphaFold_coloring.png

AlphaFold_coloring.png​

[yen-li.li@…]

Added by email2trac

[Tom Goddard]

Does the AlphaFold coloring panel ever show? For instance if you just start ChimeraX, use menu Tools / Structure Prediction / AlphaFold and press Coloring, does it appear? It does for me on Windows and on Mac. I suspect what you saw is a rare bug in the Qt window toolkit that ChimeraX uses where it does not place a new panel properly. Sometimes it ends up as a sliver in the upper right corner. Sometimes resizing the main window will make it appear. That problem is a Qt bug and we hope it the Qt developers will fix it in the future.

[Yen-Li.Li@…]

I tried to resize the main window and finally found it hidden in the upper right corner as you suggested. Thank you.

Yen-Li

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, September 13, 2021 4:46 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Elaine Meng <meng@cgl.ucsf.edu>; Li, Yen-Li <Yen-Li.Li@ucsf.edu>
Subject: Re: [ChimeraX] #5206: Clicking "Coloring" in AlphaFold panel does not show the coloring panel

#5206: Clicking "Coloring" in AlphaFold panel does not show the coloring panel
-------------------------------------------+-------------------------
          Reporter:  yen-li.li@…           |      Owner:  Tom Goddard
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  Structure Prediction  |    Version:
        Resolution:  nonchimerax           |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => nonchimerax


Comment:

 Does the AlphaFold coloring panel ever show?  For instance if you just
 start ChimeraX, use menu Tools / Structure Prediction / AlphaFold and
 press Coloring, does it appear?  It does for me on Windows and on Mac.  I
 suspect what you saw is a rare bug in the Qt window toolkit that ChimeraX
 uses where it does not place a new panel properly.  Sometimes it ends up
 as a sliver in the upper right corner.  Sometimes resizing the main window
 will make it appear.  That problem is a Qt bug and we hope it the Qt
 developers will fix it in the future.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5206#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[goddard@…]

Glad you figured out how to get around the problem.  I only see this about 1 in 500 times when I show a panel, very rare.  It is a bug in the Qt window toolkit that we use so we will have to rely on the developers of Qt to fix it.  We plan to update the Qt version we use after the ChimeraX 1.3 release comes out next month.