From: Barry Isralewitz (
Date: Mon Jul 12 2010 - 13:50:25 CDT


On Jul 12, 2010, at 2:19 AM, atila petrosian wrote:

> Hi vmd users
> I did simulation of protein-dna interaction by gromacs. I want to
> obtain
> contact map of this protein-dna interaction by vmd.
> I want to obtain a contact map such as one of its verticals be
> protein and
> another be dna.I used contact map plug-in
> and then VMD Seq Compare window was opened. in this windows, I set
> [protein and resid 1 to 70] in Molecule A section and [nucleic and
> resid
> 71 to 90] in Molecule B section. then I Selected "fit all", then
> "Calculate:
> Calc res-res Dists". but
> no action was occured. there is only a vertical axis of green color
> which
> lists Molecule A resiudes.
> please guide me.
> any help will highly appreciated

        After changing the Molecule B selection, have you tried re-selecting
the molecule number for Molecule A? The ContactMap plugin in this
release unfortunately still has a bug that requires this step after
changing selection info for either or both molecules. (That bug is in
the documentation, but still.. Sorry about that. ).

        Also, make sure that your selection text works as you intend,
particularly that it produces at least 1 residue. You can check
visually by cutting and pasting the selection text as a new
Representation in the Graphical Representations window, or check on
the command line by using an atomselect command and then getting
attributes of the result, e.g. $mySelection get resid .



Barry Isralewitz
Theoretical and Computational Biophysics Group
3043 Beckman, University of Illinois at Urbana-Champaign
Office Phone: (217) 244-1612