[Chimera-users] Ramachandran Plots

Eric Dawson eric.dawson at vanderbilt.edu
Fri Nov 16 06:58:07 PST 2007

There is a nice OpenGL based MD-viewer called MDdisplay (that I think
there are links to download on the AMBER website). This code was developed
in the research group of Terry Lybrand at Vanderbilt and has the features
that you are requsting. It is cross-platform running on WinX, MacOSX,
Linux, and SGI (maybe Alpha too).

To my knowledge, Chimera does not have a Ramachandran plot feature,
however MDdisplay does. It reads AMBER and Charmm trajectory files. I have
copied this email to the current author from the Lybrand group in case you
have questions about obtaining and installing the software on your system.




On Thu, 15 Nov 2007, Quinton Dowling wrote:

> Hi,
> I am interested in creating a ramachandran plot from an md trajectory.
>  Particularly I would like to track the change in phi/psi angles over
> time for specific amino acids throughout the md in a fashion that is
> easily presentable.  Is there a way to do this with Chimera?  Or any
> way at all?  Thanks a bunch.
> Quinton Dowling
> Research Computing Center
> The College of Idaho
> Caldwell ID 83605
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Eric S. Dawson, Ph.D.
CSB Computation, Education & Outreach
Research Instructor, Biochemistry
Center for Structural Biology (CSB)
Vanderbilt University
Nashville, TN 37232-8755
Tel: (615)-936-5579 (MRB III)
Tel: (615)-322-3303 (5119 SC)
Fax: (615)-936-2211

"All that is gold does not glitter, not all those who wander
  are lost." J.R.R. Tolkien - Fellowship of the Ring

More information about the Chimera-users mailing list