volume morph reverts orientation

[jaremko@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202103292307 (2021-03-29 23:07:54 UTC)
Description
volume morph reverts mrc realigned and moved maps back to original orientation

Log:
> ui mousemode right zoom

> set bgColor white

> graphics silhouettes true

> graphics silhouettes width 3

> hide all atoms

> style stick

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> show all cartoons

> show ligand target ab

> show ions atoms

> show sidechain & (ligand | ions) :< 3.5 target ab

> color /a #55c087

> color /b #ffe255

> color /c #f6986c

> color /d #6b80bc

> color /e #aa7fba

> color /g #FFC0CB

> color /h #b2b2b2

> color /i red

> color byhetero

> lighting soft

> lighting depthCue false

> cartoon suppressBackboneDisplay false

> volume all color #b2b2b2

Error running startup command 'vol all color #b2b2b2': No volumes specified  
UCSF ChimeraX version: 1.2.dev202103292307 (2021-03-29)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jaremko/Documents/cryoem/2021-03-25_x139-Hs128-DNA/Refine3D/job022/run_class001.mrc

Opened run_class001.mrc as #1, grid size 320,320,320, pixel 1.1, shown at
level 0.00546, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.007836

> volume #1 level 0.00654

> volume #1 level 0.007296

> open
> /Users/jaremko/Documents/cryoem/2021-03-26_x138-Hs145-128-60bpDNA/Refine3D/job055/run_class001.mrc
> format mrc

Opened run_class001.mrc as #2, grid size 320,320,320, pixel 1.1, shown at
level 0.00375, step 2, values float32  

> select #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.53137,-0.83764,-0.12652,437.86,-0.82872,0.54496,-0.12741,247.13,0.17567,0.037148,-0.98375,294.55

> view matrix models
> #2,-0.99188,-0.071703,0.10499,346.83,-0.069815,0.99733,0.021556,9.1917,-0.10626,0.014051,-0.99424,350.14

> view matrix models
> #2,-0.97404,-0.050809,0.22059,320.68,-0.093099,0.97817,-0.18579,51.356,-0.20633,-0.2015,-0.95751,399.28

> view matrix models
> #2,-0.96225,0.067394,0.2637,290.75,0.022339,0.98515,-0.17026,27.145,-0.27126,-0.15794,-0.94946,401.8

> ui mousemode right select

> ui mousemode right zoom

> ui tool show "Fit in Map"

Fit map run_class001.mrc in map run_class001.mrc using 40955 points  
correlation = 0.6429, correlation about mean = 0.09574, overlap = 4.262  
steps = 120, shift = 19, angle = 11.1 degrees  
  
Position of run_class001.mrc (#2) relative to run_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.98677979 -0.03267663 0.15873844 323.65384861  
-0.03788562 0.99883467 -0.02989961 7.74393040  
-0.15757644 -0.03551823 -0.98686783 383.60570325  
Axis -0.01775755 0.99970678 -0.01646292  
Axis point 177.16545948 0.00000000 178.98395679  
Rotation angle (degrees) 170.89734474  
Shift along axis -4.32090968  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.97789,-0.024501,0.20767,312.47,-0.049843,0.9918,-0.11769,25.78,-0.20308,-0.12544,-0.97109,404.69

> view matrix models
> #2,0.72007,0.69164,0.055882,-87.044,0.69032,-0.7222,0.043408,167.11,0.070381,0.007319,-0.99749,337.64

> view matrix models
> #2,0.98955,-0.08897,0.11345,-8.0841,-0.086052,-0.99583,-0.030374,364.36,0.11567,0.020295,-0.99308,326.63

Fit map run_class001.mrc in map run_class001.mrc using 40955 points  
correlation = 0.9713, correlation about mean = 0.9018, overlap = 8.325  
steps = 120, shift = 9.88, angle = 12.5 degrees  
  
Position of run_class001.mrc (#2) relative to run_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99955879 0.02796161 -0.01001856 -5.22990750  
0.02890482 -0.99335211 0.11142757 327.84608404  
-0.00683627 -0.11166800 -0.99372206 372.43796645  
Axis -0.99988935 -0.01426269 0.00422737  
Axis point 0.00000000 174.38107268 177.03379747  
Rotation angle (degrees) 173.59474201  
Shift along axis 2.12779371  
  

> ui mousemode right zoom

> select clear

> volume #2 step 1

> volume #2 level 0.008549

> volume #2 level 0.01041

> volume #1 level 0.008408

> volume #2 level 0.01319

> volume morph

Missing or invalid "volumes" argument: empty atom specifier  

> volume #1 level 0.007407

> volume #1 level 0.006295

> volume #1 level 0.006295

> volume #1 level 0.007518

> volume morph

Missing or invalid "volumes" argument: empty atom specifier  

> volume morph #1-2

Opened morph as #3, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> close #3

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> volume morph #1-2

Opened morph as #3, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> close #3

> show #!2 models

> show #!1 models

> save

Missing or invalid "fileName" argument: Expected a file name  




OpenGL version: 4.1 ATI-4.2.15
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      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
      System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.2.3 (20D91)
      Kernel Version: Darwin 20.3.0
      Time since boot: 20:45

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 Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[pett]

Reported by Matt Jaremko

[Tom Goddard]

I think this is a misunderstanding, not a bug. The volume morph command just linearly interpolates the two maps at corresponding grid points. If you move one map relative to the other for example to align them that makes no difference, it ignores the alignment. It would certainly be nicer if the command resampled the second map on the grid of the first map if the grids are not aligned, but it currently does not do that. Unfortunately it does not warn you that the grids are not aligned. So you have to use "volume resample" beforehand to interpolate the second map on the grid of the first map. This is documented in the volume morph documentation

​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#morph

I have made the volume morph command check that the grids are aligned and issue an error if they are not aligned to avoid this confusion.

I will make a separate ticket to improve the volume morph command so it can do the interpolation of the second map when the grids are not aligned.

[jaremko@…]

Hi Tom,

I did end up using the volume resample. Thanks for the reply.

Best,
Matt

[goddard@…]

Glad you got it to work.  I appreciate the bug report, the better error reporting I added will help others, and hopefully I will find time to make volume morph do the interpolation itself in the future.  I think your other  request for a volume morph slider is more important and long overdue.