[Chimera-users] Chimera with 50000 pdb files

Elaine Meng meng at cgl.ucsf.edu
Tue May 31 11:20:29 PDT 2011

Dear M,
There are a few possibilities:

(A) open the PDBs as a trajectory in our trajectory viewer, MD Movie, then in that tool, define a per-frame script that includes the measure inertia command.  Opening all those PDBs may take a lot of memory... it might not be possible to open them all at once.

(B) instead of PDBs, open the trajectory in its original format in MD Movie, then use per-frame script as above.  MD Movie understands several formats (see below), and most are more memory-efficient in Chimera than multiple PDBs.

(C) use python script to loop through all your PDB files, opening a file, running the command(s), closing, opening the next one, etc.  This would use less memory than (A) or (B).

In all cases, the information would go to the Reply Log (under Favorites in the menu), and you can save its contents to a text file.

More details:
(A) or (B).  Start MD Movie from menu, under Tools... MD/Ensemble Analysis.  Choose input format and then browse to your files.  See the MD Movie man page:

The "Startup and Input" section lists the known formats.  The "Per-Frame Scripts" section talks about how to run Chimera command(s) for each frame of the trajectory.  Your per-frame Chimera script could be something like:

measure inertia protein showEllipsoid false


(C).  Here is info on how to loop through multiple structures in Chimera using Python:

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

On May 31, 2011, at 1:54 AM, mselvaraj at mbu.iisc.ernet.in wrote:

> Dear all,
>     I have some 50000 pdbs obtained from a md simulation of my protein.  I
> would like to calculate ellipsoid (with 'measure inertia' command) around
> the protein molecule in each pdb and get their axes.  Is there a
> provision/script  in chimera to run multiple pdbs and get the axes in a
> file separately? Any suggestions on this will be helpful.  Thanks in
> advance.
> yours truly,
> M. Selvaraj,
> Graduate student,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> Bangalore 560 012.

More information about the Chimera-users mailing list