Morph volume slider option

[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
Can you add a slider option for volume morph? Currently I have to make a movie to analyze.  It would be nice to have the slider option to analyze in place.

Thanks,
Matt

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  




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

    Hardware Overview:

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      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
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      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
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    AMD Radeon Pro 5500M:

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      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
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          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]

Agree this would be nice. Have a previous ticket for this #2784.

[Tom Goddard]

Fixed.

Added a morph map slider that appears automatically when "volume morph" command used. Also added "slider" option to the "volume morph" command default True.

[jaremko@…]

Hi Todd,

Awesome, thanks. Will this be in the next daily build?

Thanks,
Matt


On Apr 2, 2021 8:39 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#4445: Morph volume slider option
----------------------------------+-------------------------
          Reporter:  jaremko@…    |      Owner:  Tom Goddard
              Type:  enhancement  |     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.

 Added a morph map slider that appears automatically when "volume morph"
 command used.  Also added "slider" option to the "volume morph" command
 default True.

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_4445-23comment-3A3&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=PHR2QCt41sAUtZE5ahDPgGr8zfk6tttADL2mwUfJgT8&s=QVxnbtf9vDyNEG0eZrx8bzBmNCxQa3pWxHBj_U6josg&e= >
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