VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 13 2007 - 11:07:50 CDT

Hi,
  The -samples option controls how many random area samples are taken
for each atom. The default is 500 samples, which ought to perform well
in typical cases.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 12, 2007 at 05:14:41PM -0400, Myunggi Yi wrote:
> 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 

-- 
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