[Chimera-users] movie making

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 3 11:53:40 PDT 2009

Hi Tanja,
I will describe a method that can be used in the current release  
(1.3) and then another newer method for which you need a recent daily  
build.  The newer method should be easier, so maybe skip to read that  

In the past I have done this by using a Chimera command script for  
the part before the morph.  That script must specify the directory  
and naming pattern for the image files.  For example,

#  session littlepmm2.py - movie segment before morphing
movie record directory /tmp/meng pattern elaine-* supersample 2
rock y 2 68; wait
wait 10
sc 1.01 20; move y -0.15 20
movie stop

That only saves several images without encoding a movie.  You could  
either create the morph before or after running the first script; if  
that model is not supposed to be shown in the first part of the  
movie, you could hide it using the Model Panel or modeldisplay  
command before running the script.

Then I set up the display as desired for the morphing part, in my  
case hiding the other models, showing the morph trajectory model, and  
changing the 2D labels.  Then using MD Movie "File... Record Movie" I  
would record that part.  The important thing is to use the SAME  
directory and naming pattern as in the first part.  Following the  
example above, you would enter the following in the "Additional  
recording options" area:

directory /tmp/meng pattern elaine-*

(the supersampling, if you wanted it, would be specified elsewhere in  
the dialog).  Then it knows to add the additional frames to the pre- 
existing ones instead of starting over at 1.  You could have another  
script after the morphing part if you wanted.  If so, it would be  
necessary to use another option when recording the morphing part.  In  
the MD Movie "File... Record Movie" dialog, you would put in the  
"Additional encoding options" area:

resetMode none

because this tool will always encode the movie, and you would need to  
prevent it from then deleting the images if the morphing were not the  
last part.  If you had another script, it would also need to specify  
the same image directory and naming pattern, of course.

Although I have not gone through the full process myself, I believe  
it is now possible to use just a single script, where the morph- 
playing part could be accomplished with the "coordset" command:
Then you don't have to worry about specifying the image file  
directory and naming pattern, or making sure the images are kept when  
a movie is encoded at some intermediate step.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 2, 2009, at 11:56 PM, Schulz-Gasch, Tanja wrote:
> Hi there, I used Chimera so far only for making pictures. Now I am  
> doing the first movie steps. I want to combine features like
> hide, show, rock,... with the MD Movie module to show a morph  
> between different protein conformations. How can this be done?
> The movie should start with the display part (using hide, show,  
> rock,...) followed by the morphing. However, when using the MD movie
> module the morph starts at frame 1.
> Thanks, Tanja

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