VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 17 2007 - 13:15:22 CDT

Hi,
  To draw the SASA sample points, you can do this:

set all [atomselect top "all"]
set some [atomselect top "resid 1 to 5"]
measure sasa 1.4 $all -restrict $some -points sasapoints
foreach pt $sasapoints {
  draw point $pt
}

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 16, 2007 at 03:19:14PM -0400, Govardhan Reddy wrote:
> Hello John,
> I have used the point flag to store the samples into a variable. How
> do I view these points using the draw command. I am having trouble
> using this command.
> For example if i have used the variable "sasapoints" to store the
> points. How do I use this variable with the command draw to view
> these points.
> Thank You
> Greddy
>
> On Apr 12, 2007, at 4:08 PM, John Stone 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 

-- 
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