[Chimera-users] making slow movie

Thomas Goddard goddard at cgl.ucsf.edu
Thu Apr 16 11:45:01 PDT 2009

Hi Elaine,

   This movie recording would be simpler if there was a Chimera command 
to play an MD trajectory.  I've long needed that for animation scripts. 
  I've added that to the list of feature requests:



Elaine Meng wrote:
> Eric's approach is MUCH better than what I suggested, especially for  
> these relatively small ensembles and if you want them to be  
> synchronized.  I would probably modify his approach slightly by  
> setting up all the display, styles, and colors beforehand and then  
> just using modeldisplay to toggle which models are shown and hidden.   
> Also, in Bala's case, each ensemble is one PDB file, so the individual  
> structures would be submodels.  The show/hide commands would look  
> something like this:
> ~modeldisp; modeldisp #0.1,1.1; wait 5
> ~modeldisp; modeldisp #0.2,1.2; wait 5
> On Apr 16, 2009, at 10:58 AM, Eric Pettersen wrote:
>> I think another approach is just to forget about MD Movie.  Open the
>> two ensembles using regular File..Open or the "open" command.
>> Position one ensemble on the left side and one on the right.  Then use
>> a script like this:
>> movie record ...
>> ~disp; disp #0,25; wait 5
>> ~disp; disp #1,26; wait 5
>> ...
>> ~disp; disp #24,49; wait 5
>> movie stop ...
>> movie encode ...
>> to record your movie.
>> --Eric
>> On Apr 16, 2009, at 10:47 AM, 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- 
>>> 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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