VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon May 09 2005 - 18:27:12 CDT

According to what I know, after reading your trajectory file, you can
automatically get the Ramachandran plot for the entire simulation. The
only thing you need to do is to open both topology and trajectory files,
go to Extensions-->Analysis-->Ramachandran plot. Then you pick the
residue you're interested in and you'll get a bunch of points, each one
representing the phi/psi angles.

Peace,
Michel

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
Of Ekta Khurana
Sent: Monday, May 09, 2005 6:08 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Rama plot

  Hi, Is there a way I can plot the phis and psis of the residues for
all
the frames instead of moving frame by frame using Rama plot in the pull
down menu to get a complete picture of which areas of the Ramachandran
plot are most densely populated.
Thanks,
Ekta 

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