VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Thu Mar 15 2007 - 17:11:27 CDT

Hi John,

Thanks. I see the {$atomselection get phi/psi} can be used to do my work.

Jianhui

On 3/15/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>