[Chimera-users] Plotting modes from PCA onto the structure
meng at cgl.ucsf.edu
Thu May 29 10:44:34 PDT 2008
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
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
> 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 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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