VMD-L Mailing List

From: Alexander Balaeff (abalaeff_at_chem.duke.edu)
Date: Sun Mar 18 2012 - 12:59:28 CDT

On Sun, 18 Mar 2012, George Tzotzos wrote:
>
> I'm trying to work out the parts of a structure that shows the
> greatest rms deviation during a trajectory as compared to the
> crystallographic structure. I couldn't see how this could be
> done by means of the RMSD trajectory tool. Probably it cannot.

George:

That is precisely the tool this could be done with. Note that you
could vary the atom selections you use for alignment and
computing RMSD. E.g., one can align two protein structures using
all C alpha atoms, but then compute the RMSD only for the
residues 10 through 59.

Through the GUI, that is done by editing the atom selection in
the RMSD trajectory tool window. To do the same through the TcL
interface, look up the "measure rmsd" command in the VMD manual.

set important_part_xray [atomselect 0 {name CA and resid 10 to 59}]
set important_part [atomselect 1 {name CA and resid 10 to 59}]
set rmsd(10_59) [measure rmsd $important_part_xray $important_part]

You can loop thus through your whole trajectory computing rmsd at
each point, where you can also loop over different parts of the
structure computing RMSD for each. Then save the data in a text
file to analyze by other-than-VMD tools (scripts, matlab) or
write short TcL analysis routines within VMD.

Good luck,

Alexander.

========================================================
                Dr. Alexander Balaeff
  Department of Chemistry Phone: (919) 660-1634
  Duke University, Box 90349 FAX: (919) 660-1605
  Durham, NC 27708-0349 E-mail: abalaeff_at_duke.edu
========================================================

On Sun, 18 Mar 2012, George Tzotzos wrote:

> I'm a novice to VMD and would be most grateful for any guidance.
>
> I'm trying to work out the parts of a structure that shows the greatest rms deviation during a trajectory as compared to the crystallographic structure. I couldn't see how this could be done by means of the RMSD trajectory tool. Probably it cannot.
>
> Is there a script available that can handle this? Or an alternative plug in?
>
> Thank you in advance for any help
>
> George
>