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

Ibrahim Moustafa I.moustafa at psu.edu
Thu May 29 10:08:01 PDT 2008

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 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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