VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 17 2004 - 13:12:05 CDT

Hi,
  You can try out the version I've got posted here and use the "measure sasa"
command:
  http://www.ks.uiuc.edu/Research/vmd/alpha/zs04/

The corresponding User's Guide that documents this feature is posted here:
  http://www.ks.uiuc.edu/Research/vmd/vmd-new/ug/ug.html

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 16, 2004 at 05:35:29PM -0700, Shirley Li wrote:
> Hi John,
>
> Thank you very much for your response to my question.
>
> I would be please to use this test version. It would be appreciated if you could provide me with a copy.
>
> Thank you again for your kind help.
>
> Regards,
>
> Shirley
>
>
> John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi Shirley,
> The existing released versions of VMD don't provide a built-in feature
> for calculating solvent accessible surface area, but VMD 1.8.3 includes
> a new "measure sasa" command for this purpose. If you want a test version
> to try, I can provide one for you which has this feature.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Aug 13, 2004 at 03:14:33PM -0700, Shirley Li wrote:
> > Hello,
> >
> > Could anyone tell me how to calculate the ACCESSIBLE SURFACE AREA of a protein with VMD?
> >
> > Thank you and sorry for bothering all.
> >
> > Best regards,
> >
> > Shirley
> >
> >
> > ---------------------------------
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> --
> 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
>
>
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-- 
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