[Chimera-users] Making movies

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 19 09:37:15 PDT 2009

> Hi Elaine,
> BD simulations is brownian dynamics. Well my file is in a PDB  
> format, and basically consist of a single complex, with heteroatoms  
> living from one active site to the other. If you open the file as a  
> pdb file you will realized the heteroatoms HOH are static. But I  
> want them to be able to move from the active site of one enzyme to  
> the other in the complex.
> I was thinking that I can put the word Model, between the complex,  
> and each heteroatom HOH, so as to make the file seem to have many  
> pdb files.

Hi Neville,
Yeah, I eventually realized you meant Brownian dynamics!  But what  
matters for Chimera is the format rather than how the trajectory was  

To use "MD Movie" to play/record the trajectory, your PDB format  
options are:

(a) put each frame in a separate PDB file The file names must include  
frame numbers, and files for all intermediate frames must also be  
present. The files must not contain END records.

(b) put all the frames in one PDB file, but bracket each with MODEL  
and ENDMDL, as is done for NMR ensembles in the Protein Databank, e.g.  
1g1p.  The MODEL numbers are interpreted as frame numbers and should  
start with 1 or 0 and increment by 1.

Either way, atom names, residue names/numbers need to be the same  
between frames.

** In general, each frame should have the same number of atoms.   
However, for "weird" cases where lots of atoms stay in the same  
position (which if I understand correctly is what you have), we have  
made a special provision:  if the coordinates supplied for a frame  
represent only a subset of the atoms in the preceding frame, it will  
be inferred that the remaining atoms are present but have the same  
coordinates as in the preceding frame. Changes are cumulated in the  
forward direction and based on all frames, even when frames are  
skipped during playback.  All of the atoms must be in the first frame,  
of course.  In your case, I guess that would include the proteins plus  
the starting locations of the heteroatoms.  You might need to renumber  
the HOHs to keep their identities across the frames... looks like what  
you sent gives each position a different residue  number.

This information as well as how to play the trajectory and record it  
as a movie are in the MD Movie manual page (choose Help... User's  
Guide, click Tools tab, click link "MD Movie").

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

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