Opened 4 years ago

Closed 4 years ago

#4692 closed enhancement (fixed)

Loading coordsets does not bring up slider + related problems

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: MD/Ensemble Analysis Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC)
Description
A few issues to do with this large GROMACS .xtc coordset ("SARS-CoV-2 Spike (glycans)/model/full_centers.xtc from https://osf.io/h6re4/):

- opening it does not bring up the coordinate set slider, and unless I'm just blind there is no way via the GUI to show it after the fact. The user has to know about the "coordset slider" command
- I've had two big lock-ups (~20s hang each time) - once on `~cartoon` after `show @CA`, once after `show sel`.

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color bychain; color byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.2.3 (2021-05-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/tic20/Downloads/full_centers.xtc format xtc

Must specify a structure model to read the coordinates into  

> open /home/tic20/Downloads/prot_masses.pdb

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

> open full_centers.xtc structureModel #1

No such file/path: full_centers.xtc  

> open /home/tic20/Downloads/full_centers.xtc structureModel #1

Replaced existing frames of prot_masses.pdb #1 with 3000 new frames  

> color bychain

> usage coordset

coordset structures [indexRange] [holdSteady an atoms specifier] [pauseFrames
an integer] [loop an integer] [bounce true or false] [computeSs true or false]  
— show coordinate sets  
indexRange: index range or nothing

coordset slider structures [holdSteady an atoms specifier] [pauseFrames an
integer] [computeSs true or false]  
— show slider for coordinate sets

coordset stop [structures]  
— stop playback of coordinate sets  

> coordset #1

> coordset stop

> coordset slider #1

> hide

> show @CA

> ~cartoon

> select :830-855

1167 atoms, 1173 bonds, 75 pseudobonds, 78 residues, 2 models selected  

> show sel




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         13G         37G        305M         12G         48G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
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: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    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: 1.13.3
    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-Clipper: 0.16.0
    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: 1.2.3
    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-DevelExtras: 0.4.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    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-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 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-Phenix: 0.2
    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: 1.7.4
    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: 5.0.7
    distlib: 0.3.1
    distro: 1.5.0
    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: 2.0.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    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: 1.2.0

Attachments (1)

prot_masses.pdb​ (4.8 MB ) - added by Tristan Croll 4 years ago.
Added by email2trac

Change History (15)

in reply to:  1 ; comment:1 by Tristan Croll, 4 years ago 

Weirdly, the lock-ups happen after? the result is drawn.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 27 May 2021 14:30
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #4692: ChimeraX bug report submission

#4692: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
 ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC)
 Description
 A few issues to do with this large GROMACS .xtc coordset ("SARS-CoV-2
 Spike (glycans)/model/full_centers.xtc from https://osf.io/h6re4/):

 - opening it does not bring up the coordinate set slider, and unless I'm
 just blind there is no way via the GUI to show it after the fact. The user
 has to know about the "coordset slider" command
 - I've had two big lock-ups (~20s hang each time) - once on `~cartoon`
 after `show @CA`, once after `show sel`.

 Log:
 > alias preview_toolshed toolshed url https://cxtoolshed-
 > preview.rbvi.ucsf.edu; toolshed reload available

 > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
 > toolshed reload available

 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color bychain; color byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.2.3 (2021-05-13)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open /home/tic20/Downloads/full_centers.xtc format xtc

 Must specify a structure model to read the coordinates into

 > open /home/tic20/Downloads/prot_masses.pdb

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


 > open full_centers.xtc structureModel #1

 No such file/path: full_centers.xtc

 > open /home/tic20/Downloads/full_centers.xtc structureModel #1

 Replaced existing frames of prot_masses.pdb #1 with 3000 new frames

 > color bychain

 > usage coordset

 coordset structures [indexRange] [holdSteady an atoms specifier]
 [pauseFrames
 an integer] [loop an integer] [bounce true or false] [computeSs true or
 false]
 — show coordinate sets
 indexRange: index range or nothing

 coordset slider structures [holdSteady an atoms specifier] [pauseFrames an
 integer] [computeSs true or false]
 — show slider for coordinate sets

 coordset stop [structures]
 — stop playback of coordinate sets

 > coordset #1

 > coordset stop

 > coordset slider #1

 > hide

 > show @CA

 > ~cartoon

 > select :830-855

 1167 atoms, 1173 bonds, 75 pseudobonds, 78 residues, 2 models selected

 > show sel




 OpenGL version: 3.3.0 NVIDIA 455.32.00
 OpenGL renderer: TITAN Xp/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Dell Inc.
 Model: Precision T5600
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 Virutal Machine: none
 CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
 Cache Size: 20480 KB
 Memory:
                       total        used        free      shared
 buff/cache   available
         Mem:            62G         13G         37G        305M
 12G         48G
         Swap:          4.9G          0B        4.9G

 Graphics:
         03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102
 [TITAN Xp] [10de:1b02] (rev a1)
         Subsystem: NVIDIA Corporation Device [10de:11df]
         Kernel driver in use: nvidia
 Locale: ('en_GB', 'UTF-8')
 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: 1.4.1
     chardet: 3.0.4
     ChimeraX-AddCharge: 1.0
     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: 1.13.3
     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-Clipper: 0.16.0
     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: 1.2.3
     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-DevelExtras: 0.4.0
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.2
     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-ISOLDE: 1.2.2
     ChimeraX-Label: 1.0
     ChimeraX-LinuxSupport: 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-Phenix: 0.2
     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: 1.7.4
     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: 5.0.7
     distlib: 0.3.1
     distro: 1.5.0
     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: 2.0.0
     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
     pexpect: 4.8.0
     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
     ptyprocess: 0.7.0
     pycollada: 0.7.1
     pydicom: 2.0.0
     Pygments: 2.7.1
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
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     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.1
     pytz: 2021.1
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     requests: 2.24.0
     scipy: 1.5.2
     setuptools: 50.3.2
     sfftk-rw: 0.6.7.dev1
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     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
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 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4692>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 4 years ago

Cc: Eric Pettersen added
Component: Unassigned → MD/Ensemble Analysis
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Loading coordsets does not bring up slider + related problems
Type: defect → enhancement

comment:3 by Tom Goddard, 4 years ago

Cc: Tom Goddard added; Eric Pettersen removed
Owner: changed from Tom Goddard to Eric Pettersen

When you open the gromacs trajectory you are adding its coordinate sets to an already opened model

open /home/tic20/Downloads/full_centers.xtc structureModel #1

The slider only automatically appears when an atomic model is opened and has more than one coordinate set. It does not detect when coordinate sets get added later. I think the sanest way to handle that is that this special gromacs opener should make the slider.

The 20 second pauses on ~cartoon and "show sel" must have something to do with the data, and without the data there is no way to debug that. So provide a link to the data if you want that looked at. I don't have an idea about those pauses. The graphics does not know or care about multiple coordinate sets. Only the current coordinate set matters. So why it would take eternity to change the graphics with ~cartoon or show sel is mysterious.

comment:4 by Tom Goddard, 4 years ago

I don't have a good idea for a gui to avoid having to know the "coord slider" command if you say delete the slider and want it back. A toolbar button might be nice, but so rarely useful that I can't see it taking up toolbar space. Maybe a menu entry, but where would it be -- probably very hard to find. Maybe this is not a problem if the open command makes the slider in the first place.

comment:5 by Tristan Croll, 4 years ago

Couldn't see a way to provide a direct link to the files, but if you go to ​https://osf.io/h6re4/ you'll get a directory tree on the left on the webpage. Navigate that to find "SARS-CoV-2 Spike (glycans)/model/" and you'll find prot_masses.pdb and full_centers.xtc.

in reply to:  6 ; comment:6 by Tristan Croll, 4 years ago 

My bad - the hang-up seems to have nothing to do with the fact it's a coordset - happens with just the base PDB (attached). Only seems to happen when CA-CA pseudobonds are displayed.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 28 May 2021 10:59
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4692: Loading coordsets does not bring up slider + related problems

#4692: Loading coordsets does not bring up slider + related problems
-------------------------------------------+----------------------------
          Reporter:  Tristan Croll         |      Owner:  Eric Pettersen
              Type:  enhancement           |     Status:  assigned
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------------

Comment (by Tristan Croll):

 Couldn't see a way to provide a direct link to the files, but if you go to
 https://osf.io/h6re4/ you'll get a directory tree on the left on the
 webpage. Navigate that to find "SARS-CoV-2 Spike (glycans)/model/" and
 you'll find prot_masses.pdb and full_centers.xtc.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4692#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

prot_masses.pdb​

by Tristan Croll, 4 years ago

Attachment: prot_masses.pdb​ added

Added by email2trac

in reply to:  8 comment:7 by Tristan Croll, 4 years ago 

Minimal replication:

open prot_masses.pdb
hide
show @CA
~cartoon

Doesn't appear to be the graphics redraw itself - the display is updated, then it hangs.
________________________________
From: Tristan Croll <tic20@cam.ac.uk>
Sent: 28 May 2021 14:26
To: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #4692: Loading coordsets does not bring up slider + related problems

My bad - the hang-up seems to have nothing to do with the fact it's a coordset - happens with just the base PDB (attached). Only seems to happen when CA-CA pseudobonds are displayed.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 28 May 2021 10:59
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4692: Loading coordsets does not bring up slider + related problems

#4692: Loading coordsets does not bring up slider + related problems
-------------------------------------------+----------------------------
          Reporter:  Tristan Croll         |      Owner:  Eric Pettersen
              Type:  enhancement           |     Status:  assigned
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------------

Comment (by Tristan Croll):

 Couldn't see a way to provide a direct link to the files, but if you go to
 https://osf.io/h6re4/ you'll get a directory tree on the left on the
 webpage. Navigate that to find "SARS-CoV-2 Spike (glycans)/model/" and
 you'll find prot_masses.pdb and full_centers.xtc.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4692#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:8 by Eric Pettersen, 4 years ago

Those commands all work quickly for me using 1.2.5 on my Mac. What version and platform are you using?

in reply to:  10 comment:9 by Tristan Croll, 4 years ago 

1.2.3 in Linux. I think it might be something to do with the specific model... the glycosylated asparagine residues are named NLN (an AMBER/GLYCAM thing), and (probably because of that) aren't getting bonded to their preceding residues.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 28 May 2021 17:55
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4692: Loading coordsets does not bring up slider + related problems

#4692: Loading coordsets does not bring up slider + related problems
-------------------------------------------+----------------------------
          Reporter:  Tristan Croll         |      Owner:  Eric Pettersen
              Type:  enhancement           |     Status:  assigned
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------------

Comment (by Eric Pettersen):

 Those commands all work quickly for me using 1.2.5 on my Mac.  What
 version and platform are you using?

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4692#comment:8>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:10 by Eric Pettersen, 4 years ago

I can reproduce this behavior in 1.2.3. It's not happening in 1.2.5. Try upgrading. :-)

in reply to:  12 comment:11 by Tristan Croll, 4 years ago 

Well... that's efficient!
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 28 May 2021 18:39
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4692: Loading coordsets does not bring up slider + related problems

#4692: Loading coordsets does not bring up slider + related problems
-------------------------------------------+----------------------------
          Reporter:  Tristan Croll         |      Owner:  Eric Pettersen
              Type:  enhancement           |     Status:  assigned
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------------

Comment (by Eric Pettersen):

 I can reproduce this behavior in 1.2.3.  It's not happening in 1.2.5.  Try
 upgrading. :-)

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4692#comment:10>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:12 by Eric Pettersen, 4 years ago

Yeah, checking whether pseudobonds were in the current coordinate set (to decide on whether to label them) was slow in the case of many pseudobonds and got improved between 1.2.3 and 1.2.5.

comment:13 by Eric Pettersen, 4 years ago

Status: assigned → accepted

comment:14 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Was fixed in September of last year when the 'slider' option (default true) got added to opening trajectory formats.

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