From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Jun 04 2003 - 12:08:32 CDT

Hi,

On Wed, Jun 04, 2003 at 05:58:36PM +0200, Thomas Hedegaard Pedersen wrote:
>
> In addition, is it possible to rotate some parts of a molecule by
> specifying a new dihedral, as it is possible to use the move command
> to move atomselections by some given distance x, y, z????

Yes, in the case that the dihedral you want to rotate corresponds to
either the phi or psi backbone dihedral. phi uses the N-CA-C-N atoms,
psi uses C-N-CA-C. You can obtain phi or psi values using atom selections:

  set sel [atomselect top "resid 10 11 12 and name CA"]
  $sel get phi
  $sel get psi

All atoms in the same residue have the same phi and psi values. phi will
be zero for the first residue in a chain, and psi will be zero for the last
residue.

If you change phi or psi, the rest of the chain will be rotated around that
dihedral. In the case of phi, the N-terminus will be rotated; if you change
psi, the C-terminus will be rotated. Changing phi or psi works the same way
as the other atom selection keywords. For example, to rotate a phi angle
by 20 degrees relative to its current orientation:

  set sel [atomselect top "resid 20 and name CA"]
  set curphi [$sel get phi]
  set newphi [expr {$curphi + 20}]
  $sel set phi $newphi

Let us know if you have any more questions about using this feature.

Thanks,
Justin

>
> Thank you
>
> Stud. Polyt.
> Thomas Hedegaard Pedersen
> Department of Chemistry
> Technical University of Denmark

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys