[Chimera-users] on command scripts related to movie by chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 9 09:22:20 PDT 2015

Hi Smith,
(1) Combine the scripts into one script file (or open the second script from the first with the “open” command).  If they are Chimera command scripts, there should be a total of one “movie record [options]” (start recording) before it starts showing what you want in the movie and one “movie encode [options]” (create movie file) after all the stuff you want in the movie is done. In other words, you will probably need to edit the files so that they don’t record twice and save twice, or otherwise overlap or conflict with each other.  It makes sense if you actually look in the scripts and understand what the commands are doing and in what order; scripts are in plain text, so you can just use your favorite text editor.  You can’t just treat them as black boxes and stick them together without any modification. 


If for some reason (like you have to stop recording and do something manually in between) they must remain as two separate script files, it is possible but more complicated.  Then in the first script you have to record with a specific filename pattern and stop recording at the end, but without encoding a movie file.  Then in the second script you have to resume recording with the same filename pattern.  These are options to the movie command (see its manual page).  If you are not in this special case, it is generally simpler to put everything in one script and record only once.

(2) how to display and undisplay multiple structures is basic Chimera use, regardless of whether you are making a movie.  You just need to know which model is which so that you can specify it correctly with commands: display, ribbon, surface, modeldisplay,
for example “~modeldisp #1” to hide model 1, “modeldisp #2-4” to show models 2-4.  See the individual manual pages of those commands for explanations of what they do.  You might also want to take a look at the “getting started: commands” tutorial.


Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 8, 2015, at 6:08 PM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> I want to learn several commands on chimera movie preparation. Only read the on-line material I find I still meet some difficulty.
> Suppose I have 2 scripts, each for 1 movie. Will you please tell me by which command in the script I can link the 2 scripts so that the 2 movie will change into 1 movie?
> Suppose in Chimera I have opened 2 PDB files. Will you please show me the commands to view the structure in the first PDB, then change to view the structure of the second PDB (different from the purpose of morph)? And how about if then we see the 2 structures together, all in a single movie?
> Best regards.
> Smith

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