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

Eric Pettersen pett at cgl.ucsf.edu
Fri May 30 15:15:02 PDT 2008

Hi Ibrahim,
	As Bala pointed out, IED in VMD may well be the way to go for now.   
Also, the "porcupine needles" can be accomplished with BILD, as  
Elaine mentioned.  I've attached a script that reads a file of  
displacements and applies them to the CAs of a structure.  Obviously,  
there should be as many lines in the file as there are CAs in the  
structure.  Each line should consist of 3 numbers, the X, Y, and Z  
displacements.  Since the script only modifies the CAs, you should  
probably only be displaying the CAs -- the rest of the structure will  
be out of position.  You may need to edit the script to put in the  
name of the file with the displacements, otherwise it will use a file  
named "displacements" in the same directory as the script.  You run  
the script by simply opening it with File...Open or the "open" command.
	We are working on closer coordination between Amber and Chimera,  
with the help of Wei Zhang.  He has already contributed one tool,  
Solvate, which uses sleap to solvate a system.  Solvate is available  
in daily builds.  In the short term he hopes to write tools to add  
ions and write parmtop files.  Longer term goals are to include the  
minimization and MD functionality of NAB, and ptraj trajectory analysis.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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