Opened 5 years ago

Last modified 4 years ago

#4641 assigned enhancement

Make command to replay volume morph simpler

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

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202104030245 (2021-04-03 02:45:26 UTC)
Description
Can you add command like "vseries" or "coordset" for volume morph? There is not a scriptable method to record a video of a volume morph thats already made.

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.dev202104030245 (2021-04-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jaremko/Documents/cryoem/2021-03-26_x138-Hs145-128-60bpDNA/P105/J6/output_volume.mrc

Opened output_volume.mrc as #1, grid size 128,128,128, pixel 2.75, shown at
level 0.352, step 1, values float32  

> volume #1 level 0.3415

> save
> /Users/jaremko/Documents/cryoem/2021-03-26_x138-Hs145-128-60bpDNA/P105/J6/output_volume.png

> save
> /Users/jaremko/Documents/cryoem/2021-03-26_x138-Hs145-128-60bpDNA/P105/J6/output_volume.png
> transparentBackground true

> open
> /Users/jaremko/Documents/cryoem/2021-03-26_x138-Hs145-128-60bpDNA/Autosharpen_1/sharpened_map.ccp4
> format ccp4

Opened sharpened_map.ccp4 as #2, grid size 320,320,320, pixel 1.1, shown at
level 1.55, step 2, values float32  

> volume #2 level 3.747

> volume #2 step 1

> ui tool show "Fit in Map"

Fit map sharpened_map.ccp4 in map output_volume.mrc using 145993 points  
correlation = 0.8429, correlation about mean = 0.2433, overlap = 8.637e+05  
steps = 48, shift = 1.86, angle = 2.02 degrees  
  
Position of sharpened_map.ccp4 (#2) relative to output_volume.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99953095 -0.01924218 0.02382477 -1.40259489  
0.01882363 0.99966668 0.01766904 -5.89189016  
-0.02415682 -0.01721228 0.99956000 5.75758560  
Axis -0.49488530 0.68074768 0.54006586  
Axis point 241.73899221 0.00000000 67.93637226  
Rotation angle (degrees) 2.01962611  
Shift along axis -0.20729152  
  

> volume morph #1,2

Volume grid sizes don't match: (128, 128, 128) and (320, 320, 320)  

> volume info

Expected a density maps specifier or a keyword  

> open
> /Users/jaremko/Documents/cryoem/2021-03-26_x138-Hs145-128-60bpDNA/P105/J6/output_volume_1-1px.mrc

Opened output_volume_1-1px.mrc as #3, grid size 320,320,320, pixel 1.1, shown
at level 0.351, step 2, values float32  

> volume morph #3,2

Map positions are not the same, sharpened_map.ccp4 #2 and
output_volume_1-1px.mrc #3. Use the "volume resample" command to make a copy
of one map with the same grid as the other map.  

> volume resample #3 onGrid #2

Opened output_volume_1-1px.mrc resampled as #4, grid size 320,320,320, pixel
1.1, shown at step 1, values float32  

> volume morph #4,2

Opened morph as #5, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> close #5

> volume morph #4,2 playStep .1 frames 10 scaleFactors 1,.1

Opened morph as #5, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> volume #5 level 0.7352

> volume #5 level 0.8176

> close #5

> volume morph #4,2 playStep .1 frames 10 scaleFactors 3,.1

Opened morph as #5, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> volume #5 level 0.8085

> close #5

> volume morph #4,2 playStep .1 frames 20 scaleFactors 3,.1

Opened morph as #5, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> volume #4 level 0.3506

> volume morph #4,2 playStep .1 frames 20 scaleFactors 3,.1

Opened morph as #6, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
UnboundLocalError: local variable 'close' referenced before assignment  
  
Error processing trigger "remove models":  
UnboundLocalError: local variable 'close' referenced before assignment  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph.py", line 159, in next_frame_cb  
if not self.interpolate(next_f):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph.py", line 82, in interpolate  
fccb(self.f)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 49, in _morph_changed  
i = int(.5 + (f - im.fmin) / im.fstep)  
AttributeError: 'NoneType' object has no attribute 'fmin'  
  
Error processing trigger "new frame":  
AttributeError: 'NoneType' object has no attribute 'fmin'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 49, in _morph_changed  
i = int(.5 + (f - im.fmin) / im.fstep)  
  
See log for complete Python traceback.  
  

> volume #4 level 0.3621

> close #5

> volume #6 level 0.7686

> volume resample #1 onGrid #2

Opened output_volume.mrc resampled as #5, grid size 320,320,320, pixel 1.1,
shown at step 1, values float32  

> volume morph #6,2

Opened morph as #7, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> close #7

> close #3-6

> volume resample #1 onGrid #2

Opened output_volume.mrc resampled as #3, grid size 320,320,320, pixel 1.1,
shown at step 1, values float32  

> volume morph #4,2 playStep .1 frames 10 scaleFactors 3,.1

volume morph requires 2 or more volumes, got 1  

> volume morph #4,2 playStep .1 frames 10 scaleFactors 3,.1 slider true

volume morph requires 2 or more volumes, got 1  

> volume resample #1 onGrid #2

Opened output_volume.mrc resampled as #4, grid size 320,320,320, pixel 1.1,
shown at step 1, values float32  

> volume morph #4,2 playStep .1 frames 10 scaleFactors 3,.1

Opened morph as #5, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> volume #3 level 0.3524

> close #4-5

> volume morph #3,2 playStep .1 frames 10 scaleFactors 3,.1

Opened morph as #4, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> volume #4 level 0.5811

> surface dust all

> volume #4 level 0.691

> view name 1

> windowsize

window size 640 821  

> windowsize

window size 640 821  

> movie record

> coordset #5 1,11

No structures specified  

> coordset #5 11,1

No structures specified  

> movie stop

> movie encode /Users/jaremko/Google
> Drive/CSHL/Presentations/CryoEM_Club/2021-05-13/abinitio-final.mp4

Expected ',' or a keyword  

> volume coordset

Expected a density maps specifier or a keyword  

> vseries play #5

No volume series specified  

> vseries play #4

No volume series specified  

> volume morph #3,2 playStep .1 frames 10 scaleFactors 1.5,.05

Opened morph as #5, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
UnboundLocalError: local variable 'close' referenced before assignment  
  
Error processing trigger "remove models":  
UnboundLocalError: local variable 'close' referenced before assignment  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
  
See log for complete Python traceback.  
  

> volume #5 play

Expected a keyword  

> close #5

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
UnboundLocalError: local variable 'close' referenced before assignment  
  
Error processing trigger "remove models":  
UnboundLocalError: local variable 'close' referenced before assignment  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
  
See log for complete Python traceback.  
  

> close #4

> volume morph #3,2 playStep .05 frames 10 scaleFactors 1.5,.05

Opened morph as #4, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  

> volume morph #3,2 playStep .05 frames 20 scaleFactors 1.5,.05

Opened morph as #5, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
UnboundLocalError: local variable 'close' referenced before assignment  
  
Error processing trigger "remove models":  
UnboundLocalError: local variable 'close' referenced before assignment  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_filter/morph_gui.py", line 61, in _models_closed_cb  
if close:  
  
See log for complete Python traceback.  
  

> close #5

> close #4

> volume morph #3,2 playStep .2 frames 10 scaleFactors 1.5,.05

Opened morph as #4, grid size 320,320,320, pixel 1.1, shown at step 1, values
float32  




OpenGL version: 4.1 ATI-4.4.17
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: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.3.1 (20E241)
      Kernel Version: Darwin 20.4.0
      Time since boot: 3:45

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
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
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    cftime: 1.4.1
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    ChimeraX-AddH: 2.1.5
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    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
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    ChimeraX-ColorKey: 1.2.1
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    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
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    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
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    ChimeraX-ModelSeries: 1.0
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Change History (11)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Morph tool: local variable 'close' referenced before assignment + RFE

comment:2 by Eric Pettersen, 5 years ago

Reported by Matt Jaremko

comment:3 by Tom Goddard, 5 years ago

Thanks. This does need to be improved. But you can play a previously created volume morph using the "volume morph" command by using the "model" option:

volume morph #1,​2

volume morph #1,​2 model #3 start 0.5 frames 100 slider false

This is obscure and awkward and cumbersome having to specify #1,​2 again even though model #3 knows it is a morph between #1 and #2. A useful thing to understand is that the initial "volume morph" command does not remember the interpolated volumes -- that would take too much memory. Instead it computes them on the fly whenever you play the morph using the original volumes. So replaying an existing morph doesn't really get you anything -- the only think the existing morph remembers is which volumes it is morphing between.

Maybe an improvement would be if you could replay by saying

volume morph #3

where #3 is the already created morph. And you could add the start, step, frames options as desired.

in reply to:  4 ; comment:4 by jaremko@…, 5 years ago 

Hi Todd,

Thanks for the response. I used a similar work around, but I can't use "surface dust all" (for example) on the vol morph and then record the movie. Your solution would work at the bottom if you could provide a way to use the ’surface dust’ command.

Thanks,
Matt

comment:5 by Tom Goddard, 5 years ago

I don't follow. surface dust works fine for me

volume morph #1,​2
surface dust #3 size 10
volume morph #1,​​2 model #3 start 0.5 frames 100 slider false

The surface dust filtering updates whenever the surface changes. Maybe you are confused because "surface dust all" will not apply to models that are not yet created, "all" is just shorthand for the currently open models. So you have to run the "surface dust" command after creating the morph.

in reply to:  6 ; comment:6 by jaremko@…, 5 years ago 

Hi Todd,

I see. So the "volume morph #1,​2 model #3 start 0.5 frames 100 slider false” command works on the already created morph. I’ll give that a shot. 

Thanks,
Matt

comment:7 by Tom Goddard, 5 years ago

Yeah, the "model #3" option says to reuse the existing model #3 for the morph.

comment:8 by Tom Goddard, 5 years ago

Fixed morph slider error when closing an unrelated model.

Last edited 4 years ago by Tom Goddard (previous) (diff)

comment:9 by Tom Goddard, 4 years ago

Summary: Morph tool: local variable 'close' referenced before assignment + RFE → Make command to replay volume morph simpler
Type: defect → enhancement

in reply to:  10 ; comment:10 by jaremko@…, 4 years ago 

Thanks Tom! What was the enhancement?

Best,
Matt

On Jul 21, 2021 11:42 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#4641: Make command to replay volume morph simpler
----------------------------------+-------------------------
          Reporter:  jaremko@…    |      Owner:  Tom Goddard
              Type:  enhancement  |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Volume Data  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+-------------------------
Changes (by Tom Goddard):

 * type:  defect => enhancement


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comment:11 by Tom Goddard, 4 years ago

I just changed this ticket from "defect" (ie bug) to "enhancement", have not had time to implement anything.

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