ISOLDE cursor freeze

[wxg622@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
When working with ISOLDE, once I have linked the model with the map, I have pressed the Orient option under Graphics>Camera on the toolbar interface and since then I cannot move the coursor of ISOLDE. Not sure if it is a bug but did not find the way to fix it.

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/AF/TMP/pocket/ranked_1.pdb

Chain information for ranked_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/AF/TMP/pocket/ranked_2.pdb

Chain information for ranked_2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/AF/TMP/pocket/ranked_3.pdb

Chain information for ranked_3.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/AF/TMP/pocket/ranked_4.pdb

Chain information for ranked_4.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/AF/TMP/pocket/ranked_0.pdb

Chain information for ranked_0.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_2.pdb, chain C (#2),
sequence alignment score = 1938.9  
RMSD between 346 pruned atom pairs is 0.590 angstroms; (across all 391 pairs:
3.586)  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_3.pdb, chain C (#3),
sequence alignment score = 1919.1  
RMSD between 329 pruned atom pairs is 0.536 angstroms; (across all 391 pairs:
5.843)  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_4.pdb, chain C (#4),
sequence alignment score = 1917.3  
RMSD between 324 pruned atom pairs is 0.547 angstroms; (across all 391 pairs:
4.566)  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_0.pdb, chain C (#5),
sequence alignment score = 1911.3  
RMSD between 308 pruned atom pairs is 0.456 angstroms; (across all 391 pairs:
4.260)  
  

> matchmaker #2-5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_2.pdb, chain C (#2),
sequence alignment score = 1938.9  
RMSD between 346 pruned atom pairs is 0.590 angstroms; (across all 391 pairs:
3.586)  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_3.pdb, chain C (#3),
sequence alignment score = 1919.1  
RMSD between 329 pruned atom pairs is 0.536 angstroms; (across all 391 pairs:
5.843)  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_4.pdb, chain C (#4),
sequence alignment score = 1917.3  
RMSD between 324 pruned atom pairs is 0.547 angstroms; (across all 391 pairs:
4.566)  
  
Matchmaker ranked_1.pdb, chain C (#1) with ranked_0.pdb, chain C (#5),
sequence alignment score = 1911.3  
RMSD between 308 pruned atom pairs is 0.456 angstroms; (across all 391 pairs:
4.260)  
  

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> color #1 bychain

> show #1 atoms

> hide H

> color #1 byhetero

> close

> open
> /Users/wxg622/Desktop/NTLab/Phage/Phenix/Spike/MapBox_14/full_C3_2_box.pdb
> format pdb

Summary of feedback from opening
/Users/wxg622/Desktop/NTLab/Phage/Phenix/Spike/MapBox_14/full_C3_2_box.pdb  
---  
warnings | Ignored bad PDB record found on line 1872  
SHEET A00 ***437 ILE e 295 ASN e 301 0  
  
Ignored bad PDB record found on line 1873  
SHEET A01 ***437 ALA e 359 PHE e 363 0  
  
Ignored bad PDB record found on line 1874  
SHEET A02 ***437 TYR e 371 LYS e 377 0  
  
Ignored bad PDB record found on line 1875  
SHEET A03 ***437 THR e 405 ILE e 409 0  
  
Ignored bad PDB record found on line 1876  
SHEET A04 ***437 ASN e 412 LEU e 414 0  
  
432 messages similar to the above omitted  
  
Chain information for full_C3_2_box.pdb #1  
---  
Chain | Description  
0 8 9 | No description available  
1 2 3 x y z | No description available  
4 5 7 | No description available  
6 K M Q g n | No description available  
A B C | No description available  
AA L N X h w | No description available  
AB J T d k s | No description available  
AC AD AE AF AG AH | No description available  
BB DE FH IA R o | No description available  
BG DJ GC IF W t | No description available  
D E F | No description available  
G H P V f m | No description available  
I S c j q r | No description available  
O U e l u v | No description available  
Y Z a b i p | No description available  
  

> delete ~/r

> open /Users/wxg622/Desktop/NTLab/Phage/Maps/T4/bsplt/spike/postprocess.mrc

Opened postprocess.mrc as #2, grid size 800,800,800, pixel 1.1, shown at step
1, values float32  

> volume #2 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #2 change image level -0.006852,0 level 0.02431,0.8 level 0.0757,1

> volume #2 level 0.03375

> volume #2 step 1

> isolde start

> set selectionWidth 4

Populating font family aliases took 237 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for full_C3_2_box.pdb  
---  
Chain | Description  
1.2/r | No description available  
  

> clipper associate #2 toModel #1

Opened postprocess.mrc as #1.1.1.1, grid size 800,800,800, pixel 1.1, shown at
step 1, values float32  

> view orient

> hide H

> select clear

> view orient

> view

[Repeated 1 time(s)]




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 564.40.4~66

Software:

    System Software Overview:

      System Version: macOS 13.2 (22D49)
      Kernel Version: Darwin 22.3.0
      Time since boot: 1 day, 58 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LEN P27q-10:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version:  2.4a


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    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-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Eric Pettersen]

Reported by Aritz

[Tristan Croll]

Sounds like the orient option is resetting the center of rotation mode. Can you try the command "cofr center" and see if that fixes it?

[Tom Goddard]

The view command documentation says it sets the center of rotation mode.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html

You would need to add the "cofr false" option (view orient cofr false) to avoid setting the center of rotation mode.

[Tristan Croll]

In this case the command is being emitted by clicking a button on the
ChimeraX ribbon menu, so that’s not something I (or a user) can control.

On Wed, 1 Feb 2023 at 20:10, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

Yes I figured that. We've discussed in the past that it is rough going when you override default behaviors of ChimeraX, such as making custom mouse modes that look almost like but not quite the same as the standard ones. There is no ChimeraX API to redefine what default mouse modes are, so commands that set them have no way of setting them to your overriden modes. I guess you could detect that the mouse mode has changed and try to change it back, but this is really getting into hazardous territory possibly overriding what the user wants to do.