[Chimera-users] "docking" animation

Anindito Sen as2dz at cms.mail.virginia.edu
Fri Nov 21 15:44:26 PST 2008

Hi Elaine

In continuation of the process (mentioned below) I have generated the helix 
that needs to be added. However it seems that the helix needs to be flexed 
in some points to get a better fit. Can yo let me know how do that?


On Wed, 19 Nov 2008 10:38:37 -0800
  Elaine Meng <meng at cgl.ucsf.edu> wrote:
> On Nov 19, 2008, at 9:37 AM, Bagchi, Angshuman wrote:
>> Hi,
>> Could you please tell me how to produce animation in chimera.  
>> Actually, I have 2 proteins and would like to represent them as they  
>> are getting docked. What I mean is that I would like to move the  
>> proteins and then show that as if they are getting docked.  Can this  
>> be done with chimera?
>> Thanks
>> Ang
> Hi Ang,
> Yes, it can be done.  Here is how I would do it:
> (1) create a Chimera session that includes saved/named positions of  
> the proteins separated and the proteins docked.
> (2) figure out a set of commands that does the stuff you want in your  
> animation, which would include "reset" to gradually change from one  
> saved position to the other; put the commands in a file.  Just opening  
> the file will execute the commands.
> (3) after you are happy with what the Chimera command file does, just  
> put a "movie record" command at the top of it and a "movie encode"  
> command at the bottom, and execute it.
> Now with more details:
> (1) Open the structures of the two proteins from two separate files so  
> that they can be moved separately.  You can "freeze" a structure by  
> deactivating it, so that the mouse moves only the other structure:
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html#activedef 
> >
> Save at least two positions, one with the proteins separated, another  
> with the proteins docked together, as you want them to appear in your  
> animation.  The current position is saved using the command "savepos":
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/savepos.html 
> >
> You could even save multiple positions for more control over the path  
> the proteins will take as they are "docked" in the animation.
> There is a nice example in the online movie-making tutorial, see the  
> "Ligand flying into unbound conformation" section:
> <http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html>
> Get the display how you want it: background color, ribbons, ribbon  
> style, which atoms are shown, atom display style, colors, etc.  See  
> "tips on preparing images":
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ 
> print.html#tips>
> You might also want to add a title using 2D labels (if so, leave room  
> for it when you save the positions).
> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/2dlabels/2dlabels.html 
> >
> Save the session (File... Save session As).  It will include your  
> saved positions and any 2D labels.  Now you could exit and later  
> restart the session without losing your work.
> (2) You could either try out commands by typing them individually, or  
> by putting them in a text file (named *.com or *.cmd) and repeatedly  
> opening the file after you adjust its contents and going back to the  
> starting position.
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#cmdfile 
> >
> The "reset" command is used to go from one saved position to another.   
> It can be done abruptly in one frame or gradually over a specified  
> number of frames.  See movie-related commands for links to the manual  
> page of "reset" and other commands that can do things over a specified  
> number of frames.  Besides the "reset," you might want to do other  
> things like translate or rotate or fade in/out 2D labels with these  
> commands.
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html#moviecommands 
> >
> There are also links to a few example movie command files on that page.
> (3) Once you are happy with what the script does when you open it,  
> then you can put a "movie record" command at the top and a "movie  
> encode" command at the bottom.  See the example movie command files  
> and the "movie" command description:
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/movie.html 
> >
> I prefer this process because at the end you have a session file and a  
> command file that allow you to either reproduce the process  
> efficiently, or to make some small change without a lot of duplicated  
> effort.
> I am told that "reset" has had some problems which were just fixed, so  
> if you get a bad behavior using that command, try getting a recent  
> daily build from
> <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html>
> 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
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Dr. Anindito Sen (Ph.D)
Research Associate , Dept. of Biochemistry and Molecular Genetics University 
of Virginia
Box 800733 Charlottesville, VA 22908

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