[Chimera-users] making slow movie

Thomas Goddard goddard at cgl.ucsf.edu
Thu Apr 16 11:11:17 PDT 2009

Hi Bala,

   As Elaine said increasing the bitrate is the most direct way to 
better movie quality.  The value is in Kbits/sec and default is 2000, 
and 6000 is better but produces a movie file 3 times bigger.  Also the 
supersample option can be set to 3x3 to produce smoother lines and edges 
with no increase in file size.



Elaine Meng wrote:
> 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
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 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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