Missing tools

[bruce.milthorpe@…]

The following bug report has been submitted:
Platform:        macOS-12.7.6-x86_64-i386-64bit
ChimeraX Version: 1.9rc202411130312 (2024-11-13 03:12:11 UTC)
Description
I have recently installed ChimeraX 1.9 on my Macbook Pro and ChimeraX 1.8 on my Windows machine. For both installations only 6 items appear in the dropdown list for Structure Editing, not 15 as for old Chimera. Write DMS is not available.

Log:
UCSF ChimeraX version: 1.9rc202411130312 (2024-11-13)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/brucemilthorpe/Library/CloudStorage/OneDrive-UTS/MCT8 alphafold
> models/MCT8x2/MCT8x2cut2Hchg2.cxs" format session

Log from Thu Nov 14 08:41:15 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/brucemilthorpe/Library/CloudStorage/OneDrive-UTS/MCT8 alphafold
> models/MCT8x2/MCT8dimer_6f772.result/MCT8dimer_6f772/MCT8x2cut.pdb" format
> pdb

Chain information for MCT8x2cut.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> select: 517-539.A

Unknown command: select: 517-539.A  

> select sequence 517-539

Nothing selected  

> select /A:517-539

167 atoms, 173 bonds, 23 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /B:517-539

167 atoms, 173 bonds, 23 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save "/Users/brucemilthorpe/Library/CloudStorage/OneDrive-UTS/MCT8 alphafold
> models/MCT8x2/MCT8x2cut2r1m4up.cxs"

> surface

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to MCT8x2cut.pdb #1  
---  
notes | No usable SEQRES records for MCT8x2cut.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for MCT8x2cut.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLY 97, /B GLY 97  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 516, /B LYS 516  
796 hydrogen bonds  
/A LYS 516 is not terminus, removing H atom from 'C'  
/B LYS 516 is not terminus, removing H atom from 'C'  
6722 hydrogens added  
  

> ui tool show "Add Charges"

Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  

> save "/Users/brucemilthorpe/Library/CloudStorage/OneDrive-UTS/MCT8 alphafold
> models/MCT8x2/MCT8x2cut2Hchg2.cxs"

——— End of log from Thu Nov 14 08:41:15 2024 ———

opened ChimeraX session  

> save "/Users/brucemilthorpe/OneDrive - UTS/dock6/MCT8/MCT8x2r3up.pdb"
> relModel #1

> ui tool show Registration

> toolshed reload Write DMS

Expected one of 'all', 'available', 'cache', or 'installed' or fewer arguments  

> toolshed reload installed

> help help:contact.html




OpenGL version: 4.1 INTEL-18.8.16
OpenGL renderer: Intel(R) Iris(TM) Graphics 540
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro13,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 529.120.1.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.36f102

Software:

    System Software Overview:

      System Version: macOS 12.7.6 (21H1320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 1:11

Graphics/Displays:

    Intel Iris Graphics 540:

      Chipset Model: Intel Iris Graphics 540
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1926
      Revision ID: 0x000a
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    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: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    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
    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
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411130312
    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: 1.2.5
    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
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    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: 1.6.1
    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
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.8
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Eric Pettersen]

Hi Bruce,

Despite the fact that the ChimeraX Structure Editing menu is much shorter, some of the "missing" items are in fact available elsewhere, namely:

Adjust Torsions (a tab in the Build Structure tool)
Model/Refine Loops (in the Structure Prediction menu)
Movement Mouse Mode (in the Right Mouse toolbar tab)

A couple (Minimize Structure, Write DMS) we anticipate implementing in the next year or two. I'll open a separate ticket for Write DMS and put you on it so you will get notified when it gets implemented.
So far, we have had no requests for the others (PDB2PQR, Add Ions, Solvate) and they don't seem worth the implementation effort when compared to other features we could implement. Add Ions and Solvate would be particularly difficult because current versions of AmberTools do not offer the capabilities that these tools rely on, so we would somehow have to include an ancient version of AmberTools in ChimeraX in order to offer these tools.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Bruce.Milthorpe@…]

Thank you. General searching indicates that ChimeraX did do Write DMS, except one obscure comment from many years ago. I would be very glad to be included when Write DMS comes to ChimeraX as Chimera falls over on the surfaces of my proteins, even with workaround #2.

Cheers,
Bruce

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, 15 November 2024 at 05:31
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Bruce Milthorpe <bruce.milthorpe@uts.edu.au>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #16302: Missing tools
#16302: Missing tools
----------------------------------------+--------------------
Reporter: bruce.milthorpe@… | Owner: pett
Type: enhancement | Status: closed
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: limitation | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+--------------------
Changes (by pett):

* resolution: => limitation
* status: accepted => closed

Comment:

Hi Bruce,
Despite the fact that the ChimeraX Structure Editing menu is much
shorter, some of the "missing" items are in fact available elsewhere,
namely:

Adjust Torsions (a tab in the Build Structure tool)
Model/Refine Loops (in the Structure Prediction menu)
Movement Mouse Mode (in the Right Mouse toolbar tab)

A couple (Minimize Structure, Write DMS) we anticipate
implementing in the next year or two. I'll open a separate ticket for
Write DMS and put you on it so you will get notified when it gets
implemented.
So far, we have had no requests for the others (PDB2PQR, Add Ions,
Solvate) and they don't seem worth the implementation effort when compared
to other features we could implement. Add Ions and Solvate would be
particularly difficult because current versions of AmberTools do not offer
the capabilities that these tools rely on, so we would somehow have to
include an ancient version of AmberTools in ChimeraX in order to offer
these tools.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16302#comment:2<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16302#comment:2>>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/<https://www.rbvi.ucsf.edu/chimerax>>
ChimeraX Issue Tracker

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