Open MRC volume series using a GUI

[olibclarke@…]

The following bug report has been submitted:
Platform:        macOS-13.6-arm64-arm-64bit
ChimeraX Version: 1.7.dev202309272145 (2023-09-27 21:45:56 UTC)
Description
Hi,

Would it be possible to add a GUI option for loading a volume series in a future release? Currently for mrc files I *think* (sorry if this is wrong, I did read the docs, I promise...) this is only possible on the command line, using the "open vseries" command.

Would it perhaps be possible to add a "load as volume series" checkbox to the "File...Open" dialog, that is active when the user selects more than one model or map?

This is a frequent use case for us (and I think other single particle folks) when inspecting volume series arising from 3D variability analysis in cryosparc, as well as cryoDRGN.

Cheers
Oli 

Log:
> camera ortho

> cofr centerOfView

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"

> mousemode shift leftMode "rotate selected models"

> mousemode alt control leftMode "pick blobs"

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50

> alias project_map set bgColor black; lighting depthcue false; volume $1
> style image sdlevel 0,0 color white sdlevel 100,0.15 color white
> projectionmode 3d maximumIntensityProjection false dimTransparentVoxels
> false btcorrection true showOutlineBox false linearinterpolation true

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias selbetween ks ri

> alias helix setattr $1 res is_helix true

> alias strand setattr $1 res is_strand true

> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false

> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop

> buttonpanel Shortcuts rows 3 columns 4

> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add Model_Panel command "tool show Models"

> buttonpanel Shortcuts add Log command "tool show Log"

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  
UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_000.mrc

Opened J235_component_001_frame_000.mrc as #1, grid size 80,80,80, pixel 3.12,
shown at level 0.558, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_001.mrc

Opened J235_component_001_frame_001.mrc as #2, grid size 80,80,80, pixel 3.12,
shown at level 0.554, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_002.mrc

Opened J235_component_001_frame_002.mrc as #3, grid size 80,80,80, pixel 3.12,
shown at level 0.551, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_003.mrc

Opened J235_component_001_frame_003.mrc as #4, grid size 80,80,80, pixel 3.12,
shown at level 0.551, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_004.mrc

Opened J235_component_001_frame_004.mrc as #5, grid size 80,80,80, pixel 3.12,
shown at level 0.549, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_005.mrc

Opened J235_component_001_frame_005.mrc as #6, grid size 80,80,80, pixel 3.12,
shown at level 0.551, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_006.mrc

Opened J235_component_001_frame_006.mrc as #7, grid size 80,80,80, pixel 3.12,
shown at level 0.553, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_007.mrc

Opened J235_component_001_frame_007.mrc as #8, grid size 80,80,80, pixel 3.12,
shown at level 0.557, step 1, values float32  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_008.mrc

Opened J235_component_001_frame_008.mrc as #9, grid size 80,80,80, pixel 3.12,
shown at level 0.563, step 1, values float32  

> help volume series

> close all

> open
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_008.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_007.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_006.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_005.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_004.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_003.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_002.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_001.mrc
> /Users/oc2188/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_000.mrc

Opened J235_component_001_frame_008.mrc as #1.1, grid size 80,80,80, pixel
3.12, shown at level 0.563, step 1, values float32  
Opened J235_component_001_frame_007.mrc as #1.2, grid size 80,80,80, pixel
3.12, shown at level 0.557, step 1, values float32  
Opened J235_component_001_frame_006.mrc as #1.3, grid size 80,80,80, pixel
3.12, shown at level 0.553, step 1, values float32  
Opened J235_component_001_frame_005.mrc as #1.4, grid size 80,80,80, pixel
3.12, shown at level 0.551, step 1, values float32  
Opened J235_component_001_frame_004.mrc as #1.5, grid size 80,80,80, pixel
3.12, shown at level 0.549, step 1, values float32  
Opened J235_component_001_frame_003.mrc as #1.6, grid size 80,80,80, pixel
3.12, shown at level 0.551, step 1, values float32  
Opened J235_component_001_frame_002.mrc as #1.7, grid size 80,80,80, pixel
3.12, shown at level 0.551, step 1, values float32  
Opened J235_component_001_frame_001.mrc as #1.8, grid size 80,80,80, pixel
3.12, shown at level 0.554, step 1, values float32  
Opened J235_component_001_frame_000.mrc as #1.9, grid size 80,80,80, pixel
3.12, shown at level 0.558, step 1, values float32  

> close all




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

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      Model Identifier: Mac14,5
      Model Number: Z17J00171LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.6 (22G120)
      Kernel Version: Darwin 22.6.0
      Time since boot: 2 hours, 20 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
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          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[Eric Pettersen]

The obvious issue is that the open dialog uses a native dialog, and has no ability to add interface widgets unless we go to a non-native dialog.

An alternative would be for volume series to be a different "format" and thereby have its own entry in the list of formats.

[olibclarke@…]

Another option would be to allow the reassignment of a set of already open maps as a volume series? I think this existed in Chimera (?) but I can't see how to do it using the series command in ChimeraX...?

[Tom Goddard]

Currently you have to use the open command with the "vseries true" option.

open ~/Downloads/cryosparc_P30_J235_component_001/J235_component_001_frame_*.mrc vseries true

You can use the wildcard "*" in the file path to specify several files.

I agree it would be nice to be able to open these from the GUI. Having a check button in the Open dialog would be nicest, but as Eric commented above ChimeraX uses an operating system native Open dialog that does not allow adding extra controls.

When opening 5 or more TIFF images of the same size at once ChimeraX automatically treats it as a volume series. That was done because this is often how 3D light microscopy series are used. For 4 or fewer TIFF maps of the same size it treats them as color channels. I wonder if it makes sense to do something like this with MRC and other map files, if you open 5 or more at once then automatically treat it as a series. Not sure. It would be an annoying problem if a user does not want a series.

Having a command to convert a bunch of separate maps into a series would be good, but it is still a cumbersome way to get the series loaded.

Another option is to pop up another panel after the Open panel that asks if you want separate maps or a series. That is clumsy too.

The best we came up with in old Chimera was that its Volume Series user interface has its own Open button that always makes series. Currently we don't have a volume series gui tool in ChimeraX (just a slider that appears after a series is opened).

As often happens, we are lacking an idea for a good user interface to do this.

[olibclarke@…]

Hi Tom,

I definitely would not want Chimera to automatically treat a multi-open of MRC files as a volume series, that I am sure of - many times we want to keep them separate, even when we are loading quite a few at once.

Converting a bunch of already open maps to a series may be cumbersome but it is the best I can think of - then I can open a bunch of MRCs directly in ChimeraX, and execute something like `vseries convert #1-10` or whatever, rather than having to locate the (often convoluted) path where they are located on my computer, and select an appropriate wildcard… I would favor that in the absence of any other GUI option I think, but agree it is imperfect

Cheers
Oli

[goddard@…]

I agree that a command to make individual maps that are already open into a series, e.g. "vseries create #1-10" is a step in the right direction.

[Tom Goddard]

Here's an approach you may like to opening series. You can make a button in your button panel that runs

open browse vseries true

Using the "browse" keyword will bring up a file browser and you can choose a whole series of files and it will be opened as a series.

I still think it would be nice to add a "vseries create" command to make a series from already open individual volumes. But I think the above "open browse" will be a nicer user interface for your purposes.

[olibclarke@…]

Ah that is very helpful, thanks Tom! Much easier

Cheers
Oli

[Tom Goddard]

You are right it is only possible to open a series of MRC files as a volume series using the command-line. A GUI would be nice. That could be said for many many other command-only features. Since we have limited resources we generally leave advanced and less frequently used features as command-line only, and that would apply to this request. But maybe in the future we will make a volume series gui.