From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Feb 26 2010 - 13:44:59 CST

Hi again,

The -restrict option is working very well, except that I have contributions
coming from the boundaries of the box that the sasa algorithm thinks are
exposed to the solvent. Is there some simple way to eliminate those
contributions? The only way that comes to mind is to include an extra layer
of lipids around the edges from the periodic image, and then use restrict to
eliminate that layer. maybe there is a clever atom selection taht will do
the trick...

any ideas are greatly appreciated!

Ed

On Thu, Feb 25, 2010 at 4:00 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> Sorry for being slow to reply, I've been swamped finishing papers
> and getting some new code up and running...
>
> For 1) you would feed the list of points into 'draw' commands to
> draw them however you like.
>
> For 2) yes, the -restrict command can be used to prevent part of the
> structure from contributing. You can visualize the points to help
> you figure that out.
>
> Let us know if you need more help.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 17, 2010 at 01:40:53PM -0700, Edward Lyman wrote:
> > Hi all,
> >
> > 2 questions about vmd's built in sasa calculator:
> >
> > (1) how do i visualize the surface data after i store it using the
> -points
> > option?
> > (2) will the following command measure for me the sasa for $subsel,
> > excluding the surface area of $subsel that is occluded by $sel?
> >
> > measure sasa [atomselect top "$sel"] -restrict [atomselect top
> "$subsel"]
> >
> > Thanks!
> > Ed
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>