[chimerax-users] Morphing atomic models and volumes in a single movie

[Tom Goddard]

Hi Yazan,

  The fact that you don't see the morph map disappear with smoothed maps but you do see it disappear with unsmoothed maps suggests it is not anything in your script -- it is something related to the volume data values.  My guess would be it has to do with the "constantVolume true" option.  That is trying to adjust the threshold level to keep the enclosed volume the same.  I suspect the map disappearing means some bad threshold is chosen by the constantVolume option.  You might try without that option to see if that theory is correct.  You might also try just morphing #14 to #15 since the missing surface should happen in that case two (although it may depend on the exact enclosed volume it is keeping constant).

	Tom


> On Aug 5, 2019, at 2:32 PM, Yazan Abbas <yazan.abbas at gmail.com> wrote:
> 
> Hi, 
> 
> I am trying to create a movie that is morphing between 3 atomic models while simultaneously morphing between the 3 corresponding volumes. The following is my script for recording this movie:
> 
> set max 25
> windowsize 1080 1080
> view frame1
> movie record supersample 3
> wait 1
> volume morph #12,13,14,15 frames 181 playStep 0.005524861878453038 constantVolume true modelId #16
> perframe "surface dust #16 size 40" frames 181
> coordset #10 1,181
> wait 181
> movie stop
> movie encode test_full.mp4 quality high
> 
> There are 4 maps in my morph, but the fourth map is simply a copy of the first in order to mimic the wrap true option of the atomic model morph. I am encountering the following issue during the volume morph step: somewhere in between the morph between volume #14 and #15, the map disappears for a fraction of a second in the movie. I suspect its because of a calculation/waiting issue, because if I record the movie using filtered versions of the volumes (volume guassian sDev 2), I don't have the same issue.
> 
> Am I correct in my interpretation of the issue? Is there a way to modify my recording script to avoid this?
> 
> Thanks, 
> 
> Yazan
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