VMD-L Mailing List

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Apr 12 2007 - 16:14:41 CDT

Thank you.
Would you explain examples option?

On 4/12/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Yes, what you've got there looks correct for the use of the
> VMD 'measure sasa' command. If you want to make sure that
> you're calculating the accessible surface area for the right
> part of your structure you can use the -points flag to store the
> samples into a variable and feed them into VMD draw commands to
> visually inspect the resulting sample points. That can also be
> handy if you need to avoid internal pockets or voids and aren't sure
> if they're affecting the result. I can't say anything regarding
> the DSSP SASA method since I'm not personally familiar with it
> at this time.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Apr 12, 2007 at 11:02:14AM -0400, Myunggi Yi wrote:
> > By assigning the radii and selecting the following way,
> > I can reproduce sasa comparable with dssp.
> >
> > set prot [atomselect top "protein"]
> > set sel [atomselect top "resid 11 and chain A"]
> > measure sasa 1.4 $prot -restrict $sel
> >
> > Since the algorithms are different b/w two programs,
> > I couldn't get the exactly same numbers.
> >
> > Are these correct?
> >
> >
> >
> > On 4/11/07, Myunggi Yi <myunggi_at_gmail.com> wrote:
> > >Dear users,
> > >
> > >Can one reproduce dssp ACC value using "measure sasa"?
> > >
> > >What are the atom radii in VMD?
> > >same as dssp's? (1.4 for O, 1.65 for N, 1.87 for Ca, 1.76 for C of CO
> > >in the backbone,
> > >1.8 for all sidechain atoms, and 1.4 for water)
> > >If I load a trajectory with Amber topology, then do I use amber atom radii?
> > >
> > >Is "srad" solvent radius like 1.4 for water in dssp?
> > >
> > >I compared dssp and vmd using the same pdb file (X-ray structure from PDB).
> > >I've got much larger asas values using VMD than those using dssp program.
> > >I think the difference is not from small differences of atom radii.
> > >
> > >Since dssp report every residue ACC value, I used the following
> > >
> > >set sel [atomselect top "resid 11 and chain A"]
> > >measure sasa 1.4 $sel
> > >
> > >Even when I selected only sidechain, I got large value.
> > >
> > >Any comment will be appreciated.
> > >
> > >--
> > >Best wishes,
> > >
> > >MYUNGGI YI
> > >==================================
> > >KLB 419
> > >Institute of Molecular Biophysics
> > >Florida State University
> > >Tallahassee, FL 32306
> > >
> > >Office: (850) 645-1334
> > >http://www.scs.fsu.edu/~myunggi
> > >
> >
> >
> > --
> > Best wishes,
> >
> > MYUNGGI YI
> > ==================================
> > KLB 419
> > Institute of Molecular Biophysics
> > Florida State University
> > Tallahassee, FL 32306
> >
> > Office: (850) 645-1334
> > http://www.scs.fsu.edu/~myunggi
>
> --
> 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
> 

-- 
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi