Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#4635 closed defect (fixed)

volume series slider: list index out of range

Reported by: priit.eek@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202105130135 (2021-05-13 01:35:20 UTC)
Description
Cannot play a volume series (produced by cryoDRGN). Loaded volumes via Open dialog, then used command "vseries slider #1". Pushing the play button resulted in the error.

Log:
UCSF ChimeraX version: 1.3.dev202105130135 (2021-05-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_000.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_001.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_002.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_003.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_004.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_005.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_006.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_007.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_008.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_009.mrc

Opened vol_000.mrc as #1.1, grid size 128,128,128, pixel 2.58, shown at level
0.0294, step 1, values float32  
Opened vol_001.mrc as #1.2, grid size 128,128,128, pixel 2.58, shown at level
0.029, step 1, values float32  
Opened vol_002.mrc as #1.3, grid size 128,128,128, pixel 2.58, shown at level
0.0292, step 1, values float32  
Opened vol_003.mrc as #1.4, grid size 128,128,128, pixel 2.58, shown at level
0.0288, step 1, values float32  
Opened vol_004.mrc as #1.5, grid size 128,128,128, pixel 2.58, shown at level
0.0285, step 1, values float32  
Opened vol_005.mrc as #1.6, grid size 128,128,128, pixel 2.58, shown at level
0.0279, step 1, values float32  
Opened vol_006.mrc as #1.7, grid size 128,128,128, pixel 2.58, shown at level
0.028, step 1, values float32  
Opened vol_007.mrc as #1.8, grid size 128,128,128, pixel 2.58, shown at level
0.0279, step 1, values float32  
Opened vol_008.mrc as #1.9, grid size 128,128,128, pixel 2.58, shown at level
0.0279, step 1, values float32  
Opened vol_009.mrc as #1.10, grid size 128,128,128, pixel 2.58, shown at level
0.0289, step 1, values float32  

> vseries slider #1

Traceback (most recent call last):  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 142, in play_cb  
self.play()  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play  
s0 = ser[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play  
s0 = ser[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 142, in play_cb  
self.play()  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play  
s0 = ser[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play  
s0 = ser[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 142, in play_cb  
self.play()  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play  
s0 = ser[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play  
s0 = ser[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.23
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: Intel Core i5
      Processor Speed: 3.7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 24 GB
      Boot ROM Version: 1554.100.64.0.0
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9028)
      Kernel Version: Darwin 18.7.0
      Time since boot: 5 days 19:21

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
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    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.1
    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: 1.20
    ChimeraX-AtomicLibrary: 3.2.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
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    ChimeraX-CellPack: 1.0
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    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202105130135
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
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    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
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    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
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    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.1
    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
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    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
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    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
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    ChimeraX-Tug: 1.0
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    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
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    comtypes: 1.1.10
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Change History (8)

comment:1 by pett, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem playing volume series: list index out of range

comment:2 by Tom Goddard, 4 years ago

This ChimeraX error is because your 10 open maps are not considered to be a series. Open them with this command so they are treated like a series

open /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_00*.mrc vseries true

with the "vseries true" option at the end.

I will fix the code so it gives a clear error message instead of a traceback when the vseries command is used on maps that are not a series.

in reply to:  3 ; comment:3 by priit.eek@…, 4 years ago 

Thanks for carifying this! The current documentation suggests that volume series can be opened using the GUI as well.

Best regards,
Priit

comment:4 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed
Summary: Problem playing volume series: list index out of range → volume series slider: list index out of range

Fixed.

The vseries slider command showed a slider even when no series is specified (for instance when just maps not in series are given). I've made it warn that no series were specified and not create the slider.

I don't see where in the documentation it suggests that volume series can be opened with the GUI unless it is a TIFF series of 5 or more maps or Chimera map format hdf5 file. For example here is an explanation of the rules from the documentation.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#vseries

If you can show me the place in the documentation that suggests this I can get it fixed.

in reply to:  5 ; comment:5 by priit.eek@…, 4 years ago 

I googled for “chimerax volume series” and stumbled upon this page:

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

In the last paragraph: If a volume series is opened by choosing multiple files in the dialog from menu: File... Open, the sort order in the dialog may define the temporal order.

This suggests volume series can be opened that way. Opening volumes that way actually creates a group, which can be somewhat misleading to a user who hasn’t seen how a volume series should really look like in ChimeraX.

Thanks again for your help!
P.


On May 13, 2021, at 23:02, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#4635: volume series slider: list index out of range
----------------------------------+-------------------------
         Reporter:  priit.eek@…  |      Owner:  Tom Goddard
             Type:  defect       |     Status:  closed
         Priority:  normal       |  Milestone:
        Component:  Volume Data  |    Version:
       Resolution:  fixed        |   Keywords:
       Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
          Project:  ChimeraX     |
----------------------------------+-------------------------
Changes (by Tom Goddard):

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


Comment:

Fixed.

The vseries slider command showed a slider even when no series is
specified (for instance when just maps not in series are given).  I've
made it warn that no series were specified and not create the slider.

I don't see where in the documentation it suggests that volume series can
be opened with the GUI unless it is a TIFF series of 5 or more maps or
Chimera map format hdf5 file.  For example here is an explanation of the
rules from the documentation.

   https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fopen.html%23vseries&amp;data=04%7C01%7Cpriit.eek%40psu.edu%7C2ebbac977aba41a6923f08d91684b35d%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637565581481896707%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=9ES3l2075VIgdWFgxh1qXH5wBYudUX3N9jyKwYeCdA4%3D&amp;reserved=0

If you can show me the place in the documentation that suggests this I can
get it fixed.

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comment:6 by Tom Goddard, 4 years ago

Cc: Elaine Meng added

I see. I will ask our documentation person to clarify that. That will only work for TIFF stacks. The reasoning for it only applying to TIFF stacks is that that is the common format for 3D light microscopy time series. When using other formats like MRC it is much more likely the user is opening several electron microscopy maps that are not a series, so the default is to not treat them as a series. It would be possible to put an option in the Open panel to say to treat the files as a series. I guess with continuous EM conformations as obtained from cryoDRGN and other methods this may start to become more common.

comment:7 by Tom Goddard, 4 years ago

Elaine, could you change "If a volume series is opened by choosing multiple files in the dialog from menu: File... Open, the sort order in the dialog may define the temporal order." in the volume series description on page https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html to indicate it only applies to TIFF files? Or I can do it if you like.

in reply to:  8 ; comment:8 by Elaine Meng, 4 years ago 

No problem for me to change it.  I inserted the word "TIFF" but it you want it changed further, let me know.  Preview version: <https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/trajectories.html>
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