[Chimera-users] Secondary Structures in MD data

Simon Sham Simon.Sham at USU.Edu
Wed Jun 1 10:02:23 PDT 2011

Hi Elaine,
Thank for the info. I will try what you suggested. 


From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Wednesday, June 01, 2011 10:34 AM
To: Simon Sham
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Secondary Structures in MD data

Hi Simon,
I don't know what exactly you mean by "analyze," but there is a command "ksdssp" for assigning secondary structure.  You could run that command on each frame of your trajectory.

Chimera has a tool for trajectory viewing and analysis, MD Movie.  You would first need to have or generate one of the formats that it knows, see "Startup and Input" in the man page:

MD Movie is in the menu under Tools... MD/Ensemble Analysis.  Choose input format and then browse to your files.  With MD Movie you can "play" the trajectory frame by frame or continuously, record as a movie, etc.   You can define a Chimera script to be run at each frame (see "Per-Frame Scripts" in the man page, link above).  The script could be as simple as just the command "ksdssp," or it could do lots of other stuff too.

Alternatively, if your trajectory is really large, many frames with many atoms, and it takes too much memory to put the whole thing in MD Movie, you could instead use a python script to loop through your structures, where each one is a separate PDB file, as discussed in this recent post.  You would have to generate these PDB files first.

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 Jun 1, 2011, at 7:08 AM, Simon Sham wrote:

> Hi,
> I am interested in analysizing the secondary structures from a period of MD trajectories. Is it possible to do that in Chimera?
> Thanks for your insight.
> Best,
> Simon

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