Dear Ibrahim, Try to use IED Plugin in VMD to analyze your PCA output. In fact there is a server that can produce the arrows (you want) that can show the direction and magnitude of the displacement along a Eigen vector. But i guess the server works on gromacs output only. A month ago, i posted the same query to Chimera (Analyzing PCA with chimera). I thank Elaine for his support. I would surely send some samples files of PCA analysis done with PTRAJ. I think addition of this analysis facility in Chimera is surely going to help all chimeran's a lot. Bala -----Original Message----- From: chimera-users-bounces@cgl.ucsf.edu on behalf of chimera-users-request@cgl.ucsf.edu Sent: Fri 5/30/2008 12:30 AM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 61, Issue 27 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Plotting modes from PCA onto the structure (Ibrahim Moustafa) 2. Re: Plotting modes from PCA onto the structure (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 May 2008 13:08:01 -0400 From: Ibrahim Moustafa <I.moustafa@psu.edu> Subject: [Chimera-users] Plotting modes from PCA onto the structure To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Message-ID: <C4645B32.132A%I.moustafa@psu.edu> Content-Type: text/plain; charset="us-ascii" 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