VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 04 2010 - 10:50:11 CST

Hi,
  If you're getting surface area due to periodic boundaries, the easiest
solution (at present) would be to replicate the structure across the
boundary before doing the calculation, or use the PBC tools plugins to
unwrap the parts of the structure crossing the boundary. I hope to implement
handling of periodic cells in the SASA calculation, but it I haven't started
working on it yet.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 26, 2010 at 12:44:59PM -0700, Edward Lyman wrote:
> 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/ Fax: 217-244-6078 

-- 
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