[Chimera-users] Plotting modes from PCA onto the structure

Elaine Meng meng at cgl.ucsf.edu
Thu May 29 10:44:34 PDT 2008

Hi Ibrahim,
I don't write code myself and cannot promise (given time constraints)  
that others will work on this, but it would help if you could send us  
some example files:  perhaps a PCA file and the structure snapshot  
that is the basis for the displacements, and any other files that you  
think are relevant (are the trajectory and prmtop also needed to show  
the results?).  You could send them just to me and I would share them  
as needed.

Are your PCA results from PTRAJ?  I know that several programs and  
web servers do similar PCA or NM calculations, and probably each  
produces a different output format.

You may want to take a look at converting your PCA results file into  
lines and arrows in the BILD format. Simply opening the file in  
Chimera displays the objects.  This format is extremely simple and is  
documented here, including an example file:

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote:

> Dear Chimera support,
>   I hope Chimera (with  supporting scripts) can be used to make the  
> figures described below:
>      I want to make a figure to display the different modes  
> obtained from PCA analysis (on MD trajectory obtained from AMBER)  
> as different snapshots of the structure under study.
>  To explain it more, I have a file containing the displacement in  
> X, Y, Z for each C-alpha in a column format. Is there a simple  
> script that can add the displacement vectors to the x, y, z  
> coordinates of the original structure? So the new structure with  
> modified C-alpha can be plotted representing a particular mode in  
> Chimera.
>    Also, related to the same point, is it possible to represent the  
> vectors at each C-alpha as arrows/porcupine needle in Chimera?
> P.S. It would be great if Chimera can add features to represent  
> these kind of figures from PTRAJ output or similar analysis  
> programs used in MD simulation. Especially, Chimera support  
> analysis of AMBER trajectory.
>   Thanks in advance for your great support,
>      Ibrahim
> -- 
> Ibrahim M. Moustafa, Ph.D.
> Biochemistry and Molecular Biology Dept.
> 201 Althouse Lab., University Park,
> Pennsylvania State University
> PA 16802
> Tel. (814) 863-8703
> Fax (814) 865-7927

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