VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 30 2014 - 22:42:45 CDT

Hi,
  The two options I would suggest are either to
parse the output file generated by the plugin, and draw
geometry using the "draw" commands within your own script,
or read the source code for the saltbr plugin and modify it to
be able to draw the salt bridges rather than (or in addition to)
outputting them to a file. Either approach is going to be a
do-it-yourself project, but I think that this is a pretty simple
plugin if I recall correctly, so you may be able to do it without
too much trouble if you're familiar with VMD scripting.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jun 14, 2014 at 07:33:44PM -0500, Mitul Saha wrote:
> Hi everybody,
>
> So I know how to compute salt bridges from here:-
> http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/
>
> Now, how do i visualize them on VMD after computing them using above link?
>
> Thanks,
> Mitul 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/