Plotting modes from PCA onto the structure
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
Hi Ibrahim, 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 as needed. 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: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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
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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu  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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
Ibrahim Moustafa