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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