VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 16:23:28 CDT

Hi,
  Take a look at the Ramachandran plot tool in VMD 1.8.5.
Axel Kohlmeyer added a feature which computes a ramachandran
histogram over an entire trajectory, and displays it as a
3-D histgram of phi/psi angles over the trajectory. You can
get this simply by pressing the "Create 3-D Histogram" button.
If you're looking for text output or something more customizable
for your own purpose, I'd recommend reading the Tcl script that
implements the Ramaplot plugin and modify it for your own purposes.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 15, 2007 at 04:16:21PM -0500, Jianhui Tian wrote:
> Hi,
>
> I want to export the ramachandran data for all the protein residues and plot
> all the (phi, psi) angles over the trajectory in one plot rather than one
> plot per residue using "print to file". How to do that? Or what's the code
> for calculating the phi psi angle if you know the four backbones atoms?
> Thanks.
>
> Jianhui 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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