[chimerax-users] Unable to run the option region all

[Tom Goddard]

Hi Edoardo,

  I'm not sure why one example works while the other does not.  But in either case you would need a "wait 1" after the final "volume region all" command and before encoding a movie otherwise the result of that command will not be rendered in the movie.

  It may be that the wait after your "volume all planes z,1604,1594; wait 10" is the problem.  You are showing 11 planes but waiting for only 10.  Then it goes on to do "volume region all", and after that it shows the last plane.  So you need at least "wait 11", might even try longer wait like "wait 15".

	Tom


  

> On Jul 9, 2022, at 3:05 AM, Edoardo D Imprima via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I saved two sessions with different data to make a movie using the same command lines. However, I am not able to obtain the same result when I use the command volume region.
> 
> In one instance Chimerax renders the whole 3D volumes I selected with “volume #x-y region all". In a second session, with different data but virtually the same commands, the rendering halts at the step before (~disp #1). I am puzzled because in both instances the logs show the command  “volume #x-y region all” as executed. And, in the “faulty session" if I manually input the same command that I passed through the script it eventually shows the complete regions of the volumes. 
> 
> Could you please help me to understand what am I doing wrong? I am using ChimeraX 1.4 on Linux. I am pasting here the piece of the scripts that work and do not respectively,
> 
> Many thanks in advance,
> 
> Edoardo
> 
> Working
> fly p2 p1 100; wait;  
> volume #2 show style surface level 0.8 color #5555ff;
> volume #3 show style surface level 0.8 color #aa557f;
> volume #4 show style surface level 0.8 color #f514fd;
> volume #5 show style surface level 0.8 color #11ffcc;
> volume #6 show style surface level 0.8 color #ff9429;
> volume #2-6 transparency 0.8; 
> wait 20;
> volume all planes z,1344,60; wait 1284; 
> ~disp #1; 
> volume #2-6 region all; 
> 
> Faulty
> fly p1 p2 100; wait;
>  volume #2 show style surface level 0.8 color #5555ff;
> volume #3 show style surface level 0.8 color #aa557f;
> volume #4 show style surface level 0.8 color #f514fd;
> volume #5 show style surface level 0.8 color #11ffcc;
> volume #2-5 transparency 0.5; 
> wait 20;
> volume all planes z,1604,1594; wait 10;
> ~disp #1;
> volume #2-5 region all;
> ------------------------------------------------------
> Dr. Edoardo D'Imprima
> Postdoctoral fellow
> Structural and Computational Biology Unit
> EMBL Heidelberg - Mahamid Group
> Meyerhofstraße 1
> 69117 Heidelberg
> Germany
> 
> Phone: +49 6221 387-8531
> 
> <image.jpeg>
> 
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