Opened 4 years ago

Closed 4 years ago

#5420 closed defect (fixed)

restore session in older ChimeraX

Reported by: ira.lacdao@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
i tried opening a chimera session from a collaborator.
log shows this:
open C:/Users/ik/Downloads/Composit_model.cxs
To Restore session:
update Atomic bundle to version 1.29.1 or newer (have 1.13.2)
Unable to restore session: need to update bundle

I cannot find 'Atomic' in the the toolshed list.

How can i fix this issue?


Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/ik/Downloads/Composit_model.cxs

> To Restore session:
>
>   * update Atomic bundle to version 1.29.1 or newer (have 1.13.2)
>

Unable to restore session: need to update bundle  

> toolshed show

> show # target m

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> toolshed show

> toolshed show

> help help:quickstart

> open C:/Users/ik/Downloads/Composit_model.cxs

> To Restore session:
>
>   * update Atomic bundle to version 1.29.1 or newer (have 1.13.2)
>

Unable to restore session: need to update bundle  

> toolshed list

List of installed bundles:  

  * AddCharge (1.0.1): Add partial charges to atoms
  * AddH (2.1.6): Add hydrogens
  * AlignmentAlgorithms (2.0): Sequence alignment algorithms
  * AlignmentHdrs (3.2): Alignment header support
  * AlignmentMatrices (2.0): Sequence alignment similarity matrices
  * Alignments (2.1): Sequence alignment support
  * AmberInfo (1.0): Provide information about AmberTools installation
  * Arrays (1.0): C++ library for parsing numpy arrays
  * Atomic (1.13.2): Atomic-structure functionality
  * AtomicLibrary (3.1.3): Atomic-structure C++ library
  * AtomSearch (2.0): 3D atom search
  * AtomSearchLibrary (1.0): 3D atom search support library
  * AxesPlanes (2.0): Depict axes or planes
  * BasicActions (1.1): Basic actions for user-defined specifier names
  * BILD (1.0): BILD file reader
  * BlastProtein (1.1): Search PDB/NR using BLAST
  * BondRot (2.0): Bond rotation support
  * BugReporter (1.0): Report bugs when an error occurs
  * BuildStructure (2.5.2): Create/modify structures
  * Bumps (1.0): Find protrusions in density maps
  * ButtonPanel (1.0): Create custom user interface panels
  * CageBuilder (1.0): Build polygonal meshes for oligomeric molecular assemblies
  * CellPack (1.0): Fetch cellPACK models from web
  * Centroids (1.1): Depict centroid of atoms
  * ChemGroup (2.0): Detect chemically functional groups
  * Clashes (2.1): Find clashes/contacts in structures
  * ColorActions (1.0): Simple interface for coloring objects
  * ColorGlobe (1.0): Show directional resolution colored sphere
  * ColorKey (1.2.1): Add color key to graphics
  * CommandLine (1.1.4): Command line support
  * ConnectStructure (2.0): Add bonds to structures that lack them
  * Contacts (1.0): Display chain contact maps
  * Core (1.2.5): ChimeraX Core Package
  * CoreFormats (1.0): ChimeraX session support
  * coulombic (1.1.1): Compute/show electrostatic potential
  * Crosslinks (1.0): Analyze crosslinks
  * Crystal (1.0): Crystal symmetries
  * CrystalContacts (1.0): Show contacting asymmetric units in a crystal
  * DataFormats (1.1): Data format management
  * Dicom (1.0): Read medical imaging and segmentations in DICOM format
  * DistMonitor (1.1.3): Interactive distance display
  * DistUI (1.0): Distance measurement user interface
  * Dssp (2.0): Compute/assign secondary structure
  * EMDB-SFF (1.0): EMDB SFF file reader
  * ExperimentalCommands (1.0): Experimental commands
  * FileHistory (1.0): File History Panel
  * FunctionKey (1.0): Assign function keys to run commands
  * Geometry (1.1): Vector and coordinate system routines
  * gltf (1.0): Read/write glTF 3d scene files
  * Graphics (1.0): OpenGL graphics rendering
  * Hbonds (2.1): Identify hydrogen bonds in and among structures
  * Help (1.1): Show ChimeraX Help
  * HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
  * IHM (1.0): Integrative Hybrid Models file reader
  * ImageFormats (1.1): Support for saving images
  * IMOD (1.0): IMOD model file reader
  * IO (1.0.1): Python convenience input/output functions
  * Label (1.0): Add text labels to graphics
  * ListInfo (1.1.1): Report attributes for selected atomic data
  * Log (1.1.2): Log support
  * LookingGlass (1.1): LookingGlass holographic display
  * Maestro (1.8.1): Maestro reader
  * Map (1.0.2): Density maps
  * MapData (2.0): Volume data file formats
  * MapEraser (1.0): Map eraser
  * MapFilter (2.0): Operations on maps
  * MapFit (2.0): Fit molecules into maps
  * MapSeries (2.0): Volume series
  * Markers (1.0): Place markers on density maps
  * Mask (1.0): Mask a volume to a surface
  * MatchMaker (1.2.1): Superimpose structures
  * MDcrds (2.2): Molecular dynamics support
  * MedicalToolbar (1.0.1): Toolbar for medical image analysis
  * Meeting (1.0): Shared interactive VR sessions.
  * MLP (1.1): Molecular lipophilicity calculation
  * mmCIF (2.3): mmCIF format read/write
  * MMTF (2.1): MMTF format read/write
  * Modeller (1.0.1): Interface to Modeller
  * ModelPanel (1.0.1): ChimeraX Model Panel
  * ModelSeries (1.0): Display sequences of models one by one
  * Mol2 (2.0): Mol2 reader/writer
  * Morph (1.0): Morph atomic structures
  * MouseModes (1.1): Provide right button mouse mode tool
  * Movie (1.0): Commands to record movies
  * Neuron (1.0): Read SWC neuron trace files
  * Nucleotides (2.0.1): Create nucleotide-specific displays
  * OpenCommand (1.5): Manages 'open' command extensibility
  * PDB (2.4.1): PDB format read/write
  * PDBBio (1.0): PDB biological assembly fetch
  * PDBLibrary (1.0.1): C++ PDB support
  * PDBMatrices (1.0): Crystal and biological unit matrices
  * PickBlobs (1.0): Measure and color blobs
  * Positions (1.0): Read and write model position matrices
  * PresetMgr (1.0.1): Preset management
  * PubChem (2.0.1): PubChem fetch
  * ReadPbonds (1.0): Read in pseudobonds from a file
  * Registration (1.1): Register ChimeraX
  * RemoteControl (1.0): Control ChimeraX from other apps
  * ResidueFit (1.0): Display fit of residues to density map
  * RestServer (1.1): Starts REST server to execute commands from network requests
  * RNALayout (1.0): Make RNA models
  * RotamerLibMgr (2.0): Manage rotamer libraries
  * RotamerLibsDunbrack (2.0): Dunbrack rotamer library
  * RotamerLibsDynameomics (2.0): Dynameomics rotamer library
  * RotamerLibsRichardson (2.0): Richardson rotamer libraries
  * SaveCommand (1.4): Manages 'save' command extensibility
  * SchemeMgr (1.0): HTTP scheme management
  * SDF (2.0): SDF file reader
  * Segger (1.0): Segment map
  * Segment (1.0): Watershed segment calculation
  * SeqView (2.3): Sequence viewer
  * Shape (1.0.1): Make models for geometric shapes
  * Shell (1.0): Interactive Python shell
  * Shortcuts (1.0): Button and keyboard shortcuts
  * ShowAttr (1.0): Render/select by attribute
  * ShowSequences (1.0): Choose/show structure sequences
  * SideView (1.0): Side view of scene
  * Smiles (2.0.1): SMILES fetch
  * SmoothLines (1.0): Smooth network of lines
  * SpaceNavigator (1.0): Space Navigator device support
  * StdCommands (1.3.1): Standard commands
  * STL (1.0): STL file read/write
  * Storm (1.0): STORM file reader
  * Struts (1.0): struts for 3D printing
  * Surface (1.0): Surface calculations
  * SwapAA (2.0): Swap amino acid
  * SwapRes (2.1): Swap residue side chains
  * TapeMeasure (1.0): Tape measure mouse mode
  * Test (1.0): simple regression test
  * Toolbar (1.0.1): Toolbar
  * ToolshedUtils (1.2): Toolshed bundle utilities
  * Tug (1.0): Tug on atoms with molecular dynamics
  * UI (1.7.6): ChimeraX user interface
  * uniprot (2.1): UniProt database support
  * UnitCell (1.0): Show crystal unit cell
  * ViewDockX (1.0): Analyze ligand-receptor docking results
  * Vive (1.1): Virtual reality headset support
  * VolumeMenu (1.0): Volume menu
  * VTK (1.0): Legacy VTK file reader and writer
  * WavefrontOBJ (1.0): Wavefront OBJ file read/write
  * WebCam (1.0): Combine camera video with graphics
  * WebServices (1.0): Web service and HTTP request support
  * Zone (1.0): Mouse mode to show atom and map zones

  

> help help:contact.html




OpenGL version: 3.3.0 NVIDIA 461.40
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Microsoft Corporation
Model: Surface Book 2
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 17,092,874,240
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
OSLanguage: en-US
Locale: ('en_CA', 'cp1252')
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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    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: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

in reply to:  1 ; comment:1 by Ira.Lacdao@…, 4 years ago 

Hi,

I managed to solve the issue. Had to use the latest ChimeraX daily build.

Thanks,
Ira
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Saturday, October 16, 2021 1:44 PM
To: Ira Lacdao (CUSM) <Ira.Lacdao@MUHC.MCGILL.CA>
Subject: [ChimeraX] #5420: ChimeraX bug report submission


Avertissement automatisé : Ce courriel provient de l'extérieur de votre organisation. Ne cliquez pas sur les liens et les pièces jointes si vous ne reconnaissez pas l'expéditeur.



#5420: ChimeraX bug report submission
--------------------------+-----------------------------
 Reporter:  ira.lacdao@…  |                Type:  defect
   Status:  new           |            Priority:  normal
Component:  Unassigned    |          Blocked By:
 Blocking:                |  Notify when closed:
--------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Windows-10-10.0.19041
 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
 Description
 (Describe the actions that caused this problem to occur here)
 i tried opening a chimera session from a collaborator.
 log shows this:
 open C:/Users/ik/Downloads/Composit_model.cxs
 To Restore session:
 update Atomic bundle to version 1.29.1 or newer (have 1.13.2)
 Unable to restore session: need to update bundle

 I cannot find 'Atomic' in the the toolshed list.

 How can i fix this issue?


 Log:
 UCSF ChimeraX version: 1.2.5 (2021-05-24)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open C:/Users/ik/Downloads/Composit_model.cxs

 > To Restore session:
 >
 >   * update Atomic bundle to version 1.29.1 or newer (have 1.13.2)
 >

 Unable to restore session: need to update bundle

 > toolshed show

 > show # target m

 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword

 > toolshed show

 > toolshed show

 > help help:quickstart

 > open C:/Users/ik/Downloads/Composit_model.cxs

 > To Restore session:
 >
 >   * update Atomic bundle to version 1.29.1 or newer (have 1.13.2)
 >

 Unable to restore session: need to update bundle

 > toolshed list

 List of installed bundles:

   * AddCharge (1.0.1): Add partial charges to atoms
   * AddH (2.1.6): Add hydrogens
   * AlignmentAlgorithms (2.0): Sequence alignment algorithms
   * AlignmentHdrs (3.2): Alignment header support
   * AlignmentMatrices (2.0): Sequence alignment similarity matrices
   * Alignments (2.1): Sequence alignment support
   * AmberInfo (1.0): Provide information about AmberTools installation
   * Arrays (1.0): C++ library for parsing numpy arrays
   * Atomic (1.13.2): Atomic-structure functionality
   * AtomicLibrary (3.1.3): Atomic-structure C++ library
   * AtomSearch (2.0): 3D atom search
   * AtomSearchLibrary (1.0): 3D atom search support library
   * AxesPlanes (2.0): Depict axes or planes
   * BasicActions (1.1): Basic actions for user-defined specifier names
   * BILD (1.0): BILD file reader
   * BlastProtein (1.1): Search PDB/NR using BLAST
   * BondRot (2.0): Bond rotation support
   * BugReporter (1.0): Report bugs when an error occurs
   * BuildStructure (2.5.2): Create/modify structures
   * Bumps (1.0): Find protrusions in density maps
   * ButtonPanel (1.0): Create custom user interface panels
   * CageBuilder (1.0): Build polygonal meshes for oligomeric molecular
 assemblies
   * CellPack (1.0): Fetch cellPACK models from web
   * Centroids (1.1): Depict centroid of atoms
   * ChemGroup (2.0): Detect chemically functional groups
   * Clashes (2.1): Find clashes/contacts in structures
   * ColorActions (1.0): Simple interface for coloring objects
   * ColorGlobe (1.0): Show directional resolution colored sphere
   * ColorKey (1.2.1): Add color key to graphics
   * CommandLine (1.1.4): Command line support
   * ConnectStructure (2.0): Add bonds to structures that lack them
   * Contacts (1.0): Display chain contact maps
   * Core (1.2.5): ChimeraX Core Package
   * CoreFormats (1.0): ChimeraX session support
   * coulombic (1.1.1): Compute/show electrostatic potential
   * Crosslinks (1.0): Analyze crosslinks
   * Crystal (1.0): Crystal symmetries
   * CrystalContacts (1.0): Show contacting asymmetric units in a crystal
   * DataFormats (1.1): Data format management
   * Dicom (1.0): Read medical imaging and segmentations in DICOM format
   * DistMonitor (1.1.3): Interactive distance display
   * DistUI (1.0): Distance measurement user interface
   * Dssp (2.0): Compute/assign secondary structure
   * EMDB-SFF (1.0): EMDB SFF file reader
   * ExperimentalCommands (1.0): Experimental commands
   * FileHistory (1.0): File History Panel
   * FunctionKey (1.0): Assign function keys to run commands
   * Geometry (1.1): Vector and coordinate system routines
   * gltf (1.0): Read/write glTF 3d scene files
   * Graphics (1.0): OpenGL graphics rendering
   * Hbonds (2.1): Identify hydrogen bonds in and among structures
   * Help (1.1): Show ChimeraX Help
   * HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
   * IHM (1.0): Integrative Hybrid Models file reader
   * ImageFormats (1.1): Support for saving images
   * IMOD (1.0): IMOD model file reader
   * IO (1.0.1): Python convenience input/output functions
   * Label (1.0): Add text labels to graphics
   * ListInfo (1.1.1): Report attributes for selected atomic data
   * Log (1.1.2): Log support
   * LookingGlass (1.1): LookingGlass holographic display
   * Maestro (1.8.1): Maestro reader
   * Map (1.0.2): Density maps
   * MapData (2.0): Volume data file formats
   * MapEraser (1.0): Map eraser
   * MapFilter (2.0): Operations on maps
   * MapFit (2.0): Fit molecules into maps
   * MapSeries (2.0): Volume series
   * Markers (1.0): Place markers on density maps
   * Mask (1.0): Mask a volume to a surface
   * MatchMaker (1.2.1): Superimpose structures
   * MDcrds (2.2): Molecular dynamics support
   * MedicalToolbar (1.0.1): Toolbar for medical image analysis
   * Meeting (1.0): Shared interactive VR sessions.
   * MLP (1.1): Molecular lipophilicity calculation
   * mmCIF (2.3): mmCIF format read/write
   * MMTF (2.1): MMTF format read/write
   * Modeller (1.0.1): Interface to Modeller
   * ModelPanel (1.0.1): ChimeraX Model Panel
   * ModelSeries (1.0): Display sequences of models one by one
   * Mol2 (2.0): Mol2 reader/writer
   * Morph (1.0): Morph atomic structures
   * MouseModes (1.1): Provide right button mouse mode tool
   * Movie (1.0): Commands to record movies
   * Neuron (1.0): Read SWC neuron trace files
   * Nucleotides (2.0.1): Create nucleotide-specific displays
   * OpenCommand (1.5): Manages 'open' command extensibility
   * PDB (2.4.1): PDB format read/write
   * PDBBio (1.0): PDB biological assembly fetch
   * PDBLibrary (1.0.1): C++ PDB support
   * PDBMatrices (1.0): Crystal and biological unit matrices
   * PickBlobs (1.0): Measure and color blobs
   * Positions (1.0): Read and write model position matrices
   * PresetMgr (1.0.1): Preset management
   * PubChem (2.0.1): PubChem fetch
   * ReadPbonds (1.0): Read in pseudobonds from a file
   * Registration (1.1): Register ChimeraX
   * RemoteControl (1.0): Control ChimeraX from other apps
   * ResidueFit (1.0): Display fit of residues to density map
   * RestServer (1.1): Starts REST server to execute commands from network
 requests
   * RNALayout (1.0): Make RNA models
   * RotamerLibMgr (2.0): Manage rotamer libraries
   * RotamerLibsDunbrack (2.0): Dunbrack rotamer library
   * RotamerLibsDynameomics (2.0): Dynameomics rotamer library
   * RotamerLibsRichardson (2.0): Richardson rotamer libraries
   * SaveCommand (1.4): Manages 'save' command extensibility
   * SchemeMgr (1.0): HTTP scheme management
   * SDF (2.0): SDF file reader
   * Segger (1.0): Segment map
   * Segment (1.0): Watershed segment calculation
   * SeqView (2.3): Sequence viewer
   * Shape (1.0.1): Make models for geometric shapes
   * Shell (1.0): Interactive Python shell
   * Shortcuts (1.0): Button and keyboard shortcuts
   * ShowAttr (1.0): Render/select by attribute
   * ShowSequences (1.0): Choose/show structure sequences
   * SideView (1.0): Side view of scene
   * Smiles (2.0.1): SMILES fetch
   * SmoothLines (1.0): Smooth network of lines
   * SpaceNavigator (1.0): Space Navigator device support
   * StdCommands (1.3.1): Standard commands
   * STL (1.0): STL file read/write
   * Storm (1.0): STORM file reader
   * Struts (1.0): struts for 3D printing
   * Surface (1.0): Surface calculations
   * SwapAA (2.0): Swap amino acid
   * SwapRes (2.1): Swap residue side chains
   * TapeMeasure (1.0): Tape measure mouse mode
   * Test (1.0): simple regression test
   * Toolbar (1.0.1): Toolbar
   * ToolshedUtils (1.2): Toolshed bundle utilities
   * Tug (1.0): Tug on atoms with molecular dynamics
   * UI (1.7.6): ChimeraX user interface
   * uniprot (2.1): UniProt database support
   * UnitCell (1.0): Show crystal unit cell
   * ViewDockX (1.0): Analyze ligand-receptor docking results
   * Vive (1.1): Virtual reality headset support
   * VolumeMenu (1.0): Volume menu
   * VTK (1.0): Legacy VTK file reader and writer
   * WavefrontOBJ (1.0): Wavefront OBJ file read/write
   * WebCam (1.0): Combine camera video with graphics
   * WebServices (1.0): Web service and HTTP request support
   * Zone (1.0): Mouse mode to show atom and map zones



 > help help:contact.html




 OpenGL version: 3.3.0 NVIDIA 461.40
 OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Microsoft Corporation
 Model: Surface Book 2
 OS: Microsoft Windows 10 Pro (Build 19043)
 Memory: 17,092,874,240
 MaxProcessMemory: 137,438,953,344
 CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
 OSLanguage: en-US
 Locale: ('en_CA', 'cp1252')
 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: 2020.12.5
     cftime: 1.5.0
     chardet: 3.0.4
     ChimeraX-AddCharge: 1.0.1
     ChimeraX-AddH: 2.1.6
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.13.2
     ChimeraX-AtomicLibrary: 3.1.3
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 1.1
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.5.2
     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: 1.2.1
     ChimeraX-CommandLine: 1.1.4
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.2.5
     ChimeraX-CoreFormats: 1.0
     ChimeraX-coulombic: 1.1.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.1
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.3
     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: 1.0
     ChimeraX-Hbonds: 2.1
     ChimeraX-Help: 1.1
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.0
     ChimeraX-ImageFormats: 1.1
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0.1
     ChimeraX-Label: 1.0
     ChimeraX-ListInfo: 1.1.1
     ChimeraX-Log: 1.1.2
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Maestro: 1.8.1
     ChimeraX-Map: 1.0.2
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.0
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 1.2.1
     ChimeraX-MDcrds: 2.2
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.3
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.0.1
     ChimeraX-ModelPanel: 1.0.1
     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: 2.0.1
     ChimeraX-OpenCommand: 1.5
     ChimeraX-PDB: 2.4.1
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.1
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0.1
     ChimeraX-PubChem: 2.0.1
     ChimeraX-ReadPbonds: 1.0
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     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: 1.4
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SeqView: 2.3
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.0
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.0.1
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.3.1
     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
     ChimeraX-Toolbar: 1.0.1
     ChimeraX-ToolshedUtils: 1.2
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.7.6
     ChimeraX-uniprot: 2.1
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.3
     comtypes: 1.1.7
     cxservices: 1.0
     cycler: 0.10.0
     Cython: 0.29.21
     decorator: 5.0.9
     distlib: 0.3.1
     docutils: 0.16
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 2.10.0
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.17
     imagecodecs: 2020.5.30
     imagesize: 1.2.0
     ipykernel: 5.3.4
     ipython: 7.18.1
     ipython-genutils: 0.2.0
     jedi: 0.17.2
     Jinja2: 2.11.2
     jupyter-client: 6.1.7
     jupyter-core: 4.7.1
     kiwisolver: 1.3.1
     line-profiler: 2.1.2
     lxml: 4.6.2
     lz4: 3.1.0
     MarkupSafe: 2.0.1
     matplotlib: 3.3.2
     msgpack: 1.0.0
     netCDF4: 1.5.4
     networkx: 2.5
     numexpr: 2.7.3
     numpy: 1.19.2
     numpydoc: 1.1.0
     openvr: 1.14.1501
     packaging: 20.9
     ParmEd: 3.2.0
     parso: 0.7.1
     pickleshare: 0.7.5
     Pillow: 7.2.0
     pip: 21.0.1
     pkginfo: 1.5.0.1
     prompt-toolkit: 3.0.18
     psutil: 5.7.2
     pycollada: 0.7.1
     pydicom: 2.0.0
     Pygments: 2.7.1
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.1
     pytz: 2021.1
     pywin32: 228
     pyzmq: 22.0.3
     qtconsole: 4.7.7
     QtPy: 1.9.0
     RandomWords: 0.3.0
     requests: 2.24.0
     scipy: 1.5.2
     setuptools: 50.3.2
     sfftk-rw: 0.6.7.dev1
     six: 1.15.0
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     Sphinx: 3.2.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     sphinxcontrib-devhelp: 1.0.2
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     sphinxcontrib-serializinghtml: 1.1.5
     suds-jurko: 0.6
     tables: 3.6.1
     tifffile: 2020.9.3
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     tornado: 6.1
     traitlets: 5.0.5
     urllib3: 1.25.11
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.36.0
     wheel-filename: 1.3.0
     WMI: 1.5.1

 }}}

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ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 4 years ago

Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → restore session in older ChimeraX

comment:3 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Hi Ira,

As you figured out yourself, ChimeraX 1.2.5 can't restore newer 1.3 sessions. Sorry the message you get isn't clearer about that.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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