VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 17 2003 - 12:51:20 CDT

Sanjeev,
  How are you displaying the MSMS surface and the "pdb" you are creating
from the vertices? VMD doesn't necessarily scale/center all molecules
the same way, so if you have loaded them as separate molecules, you
are probably just causing yourself headaches here. The best solution
would be to skip making a faked PDB file and make a Tcl script that uses the
VMD 'draw' commands instead. The script you'd generate would look
something like this:

draw color white
draw point { 0 0 0 }
draw point { 0 0 1 }
draw point { 0 1 0 }
draw point { 0 1 1 }
draw point { 1 0 0 }
draw point { 1 0 1 }
draw point { 1 1 0 }
draw point { 1 1 1 }

If you load your script with "play foo.tcl" while the MSMS rep/molecule
is active as the 'top' molecule in VMD, it should draw in the same
coordinate system as your MSMS. At the very least this ought to eliminate
the possibility of having different scaling going on between molecules.
Give that a try and let me know how it goes for you. If you need further
assistance, just email vmd_at_ks.uiuc.edu, as I'm not sure whether its worth
including all of VMD-L on our little script debugging adventure. :-)
At the very least we could summarize when all is finished up.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 17, 2003 at 11:48:44PM +0530, Sanjeev B.S. wrote:
> >and the socket interfaces in MSMS. If you tell me how you are attempting
> >to compare the vertices I can presumably help you get what you want.
> +++ OK, then it's possible that at this end there is some problem. I was
> generating .vert file, changing that to a PDB with each point being a
> hydrogen. Then making surface of the protein I would check. I am sending
> for your perusal an image of the o/p, and I rechked the o/p but all seems
> fine.
> The command for MSMS generation was:
> $ msms -if myset.xyzr -density 5.0 -prob 1.4 -of myset
> I have chosen the same values for MSMS surf generation in VMD.
>
> -Sanjeev
>
> 

-- 
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