VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Sep 14 2009 - 21:32:23 CDT

Hi Jorgen,
I'm not aware of a simple solution; you'll have to write a little
procedure for it. You should be able to copy most of the code from
::Molefacture::rotate_bond (in molefacture_geometry.tcl). Just feed in
your atom indices instead of using the dihedatom array, and don't bother
with the stuff at the end that updates the molefacture graphics. The
selections for atoms on the two sides of the dihedral are calculated in
the highlight_bond proc of molefacture_internals.tcl, which uses
::util::bondedsel.
Best,
Peter

Jorgen Simonsen wrote:
> Hi all,
>
> I would like to rotate the dihedral angle of one of my residues from
> 60 to 120 with 10 degrees interval. I have been looking at the
> molefracture but would like to invoke it form the command line. I am
> not quite sure how to proceed if my atom names are c1,c2,c3,c4(they
> have a dihedral angle in the moelfracture) how to change the angle by
> steps of 10 using vmd command line?
>
> Thanks in advance
>
> Best
>
> Jorgen