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
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. Best, Eric ----- 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@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) 5137 MRBIII 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
This and other types of important types of MD analysis are are my to- do list, but I really don't have a good idea as to when I'll have time to implement them. Until then, as Eric Dawson mentioned in his reply, MDdisplay offers this capability. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Nov 15, 2007, at 8:53 PM, 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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Eric Dawson -
Eric Pettersen -
Quinton Dowling