From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Thu Feb 25 2010 - 17:05:37 CST

I think that ought to do it, thanks very much. I figured the answer to (1)
would help me to answer (2).

E

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/>
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>