[Chimera-users] making slow movie

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 16 10:47:32 PDT 2009

Hi Bala,
Now to your question #2.  The short answer is no.  However, there are  
some possible approaches, requiring various levels of effort:

(A) If it is OK if the two playbacks are not exactly synchronized  
(don't need frame 1 and frame 1 together, 2 and 2, etc.),  you can  
just open the two files by starting MD Movie twice.  Then you will  
have two playback controllers.  For testing, I used NMR ensemble PDB  
entries 1g1p and 1g1z.  These have 18 structures each.  While just  
showing one frame of each (not playing through the frames), I used "mm  
#0 #1" to fit them into the same orientation.  Then I resized the  
Chimera window to make it longer horizontally and moved one model to  
the left and the other to the right.  Something like these commands  
(using version 1.4, a daily build):
move x -13 models #0
move x 13 models #1
Of course, you would also set colors, display styles, etc. as you want  
for the movie.  Because these two structures are the same size, they  
play back at about the same speed if I put the two "Playback speed"  
sliders in the same place.  I put both at the far left.  If your two  
structures don't play back at nearly the same speed, move the sliders  
to try to make them update at the same rate.  Now play back  
continuously for one ensemble.  For the other one, stop the playback,  
choose File... Record movie and proceed as you have been doing.  The  
movie will step through that ensemble, and the other one will just  
happen to be changing at the same time.  Tada!  I will send you the  
Quicktime movie from my test in a separate message.

(B) If you need frame 1 with 1, 2 with 2, etc. it is much more  
effort.   I can think of two different routes.
    (1) just open one ensemble and record with MD Movie, using  
recording options to control the name and location of the saved image  
files and the encoding option to keep those files rather than deleting  
them after encoding a movie.  Do the same for the other ensemble.   
Then with some separate image-processing program combine the first  
image from each into a new first image with both side by side, etc.  
for the whole set of saved images.  Then encode the new set of  
combined images into a movie.  This would need to be done outside of  
Chimera, but I believe you could use the software embedded in Chimera  
to do it.  I think the Reply Log shows what command is being used to  
encode the movie and you could use an analogous command in your system  
shell or terminal to do it.  I haven't done this myself, however.
   (2) instead create a combined PDB file where each MODEL has both  
structures side by side.  First you'd have to open the two files in  
Chimera, do any fitting and moving as described in (A), then save PDB  
for one ensemble "relative to" the other model.  Then there would be a  
lot of painful editing to combine the coordinates into one multi-MODEL  
file.  It would probably require renumbering so that there are not  
duplicate residues within a single MODEL.  Then open that new file  
with MD Movie as a single trajectory, proceed with recording a movie.

As for #3, I am not expert in this area.  My general impression is  
that you could start with the default settings.  If that does not look  
as nice as you want, you could try increasing the bitrate in the  
encoding options.  It is always a trade-off of size and quality,  
however (nicer looking -> bigger file).

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 Apr 16, 2009, at 3:32 AM, Bala subramanian wrote:

> Friends,
> I am using MD movie with chimera to see the motion of a single pdb  
> containing 25 models. I kept the play back speed at low value, then  
> recorded the movie. But the movie comes very fast. I guess there is  
> no related functionality between playback speed and the speed with  
> which the movie is recorded.
> 1) How can i record a movie with low playback speed.
> 2) Is it possible to split the chimera screen in to two halfes or as  
> quadrants (like in sybyl) and then load the molecules wherever we  
> want.
>   Now why i need it ?.
>  I have two pdb files (each consisiting of 25 models). If i can  
> split the chimera screen, i would like to load pdb1 left and pdb2 in  
> rigth side using MD movie, then record the movie. Any better idea  
> than this to achieve the same would be highly appreciated.
> 3) Kindly suggest me some better setting to record a movie with high  
> clarity based on your experience.
> Thanks,
> Bala

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