vseries play markers option is broken

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202010140223 (2020-10-14 02:23:41 UTC)
Description
vseries play command "markers" option is broken.  I suspect it was never ported from Chimera.

Log:
UCSF ChimeraX version: 1.2.dev202010081722 (2020-10-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> usage marker

marker markerSet position center point [radius a number] [color a color]
[coordinateSystem a coordinate-system]  
— Place a marker  
markerSet: a marker set or a model id  
Subcommands are:

  * marker change
  * marker connected
  * marker delete
  * marker fromMesh
  * marker link
  * marker segment

  

> open /Users/goddard/ucsf/data/neutrophil-vr/c7ch0step221.cmap

Opened map series c7ch0step221.cmap, 110 images, grid size 128,256,151, pixel
0.2,0.2,0.25, shown at level 285, step 1, values float32  

> vseries play #1

> ui mousemode right "mark surface"

> marker #2 position 4.294,19.92,37.29 color yellow radius 1

> marker #2 position 8.276,20.37,37.43 color yellow radius 1

> marker #2 position 15.71,23.56,33 color yellow radius 1

> vseries play #1 markers #2

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/play.py", line 114, in next_time_cb  
self.change_time(self.start_time)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/play.py", line 188, in change_time  
self.update_marker_display()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/play.py", line 284, in update_marker_display  
m.atoms.displays = False  
AttributeError: 'Atoms' object has no attribute 'atoms'  
  
Error processing trigger "new frame":  
AttributeError: 'Atoms' object has no attribute 'atoms'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/play.py", line 284, in update_marker_display  
m.atoms.displays = False  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 13 days 19:48

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
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    ChimeraX-Hbonds: 2.1
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    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
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    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
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    ChimeraX-Mask: 1.0
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[Tom Goddard]

Looks like marker notes have no support in the code. Probably because this is a really hacky way to record which frame a marker belongs to. Would probably be better to make a new marker attribute "frame" for that. Also when placing markers with the mouse they should set that frame option if placed on a map series. And support to save and restore from .cmm files will be needed.

[Tom Goddard]

Fixed.

I made vseries play use the "frame" attribute of markers. This differs from Chimera 1 where it used the "note" attribute. Placing markers with the mouse or with the marker connected command will set the frame attribute of the new markers when the markers are place on a map series. The vseries play command options markers, precedingMarkerFrames and followingMarkerFrames now work using the marker frame attribute. The frame attribute is written to cmm marker files and to session files.

[Elaine Meng]

That's great!  A couple of questions:

- Does "vseries measure" assign the frame attribute to the markers it creates? 
(that was one way, maybe the main way, to create the frame-associated markers in Chimera)


-  Since you didn't mention it, I'm guessing that the"colorRange" option of vseries, which also used marker notes for time association, is not implemented

[goddard@…]

Yes vseries measure creates centroid markers with frame numbers.
Ok, you convinced me, I've made vseries play colorRange work too.