VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 09 2015 - 17:17:24 CDT

Gianluca,
  Another possibility with large sample counts, is that we may have
exceeded the usefulness of the particular pseudo-random number generator
that code is using. If I have time, I may try an experiment with the
PDB you asked about and switch to a different PRNG algorithm and see
if it improves or has any impact. In any case, if you want a
precise SASA value, in the short-term you are likely best served
by looking at some other tools that use a different method. If you have
a chance to try Nanoshaper (which from papers I've read, has a SASA feature),
I would be curious to hear what you think:
  http://www.electrostaticszone.eu/index.php/new-nanoshaper-release-0-7/cat_view/1-nanoshaper

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 09, 2015 at 02:52:40PM -0700, Gianluca Interlandi wrote:
> Thanks John,
>
> I realized that the default value for -samples is actually 500. I
> tried 50,000 and got 10348 before and 10347 after rotating. However,
> if I increase it to 100,000 they diverge again: 10345 before and
> 10348 after rotating. It seems that 50,000 is the best value in this
> case.
>
> Gianluca
>
> On Thu, 9 Apr 2015, John Stone wrote:
>
> >Hi,
> > The simplistic SASA algorithm currently implemented in VMD uses monte carlo
> >sampling to estimate the accessible surface area. It takes a finite
> >number of samples (I forget, but the default is something like 50,000
> >samples if you don't specify a larger count) and so if you have a
> >big structure or you're unlucky, you might need to crank up the sample
> >count to improve its self-consistency. 1/50,000 error not far below
> >what you're showing there, so it would only take a few more of the random
> >samples to switch from "miss" to "hit" and that would account for the
> >difference you see.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Apr 09, 2015 at 02:17:18PM -0700, Gianluca Interlandi wrote:
> >>Dear list,
> >>
> >>I wonder why the command measure sasa does not give consistent
> >>results which should be independent whether the protein is rotated.
> >>
> >>For example, I loaded protein with PDB code 1AUQ.
> >>
> >>Then, I calculated the SASA of the entire system:
> >>
> >>measure sasa 1.4 [atomselect top all]
> >>10260.4560546875
> >>
> >>I rotated the system by 30 degrees around the y-axis:
> >>
> >>[atomselect top all] move [trans y 30]
> >>
> >>And calculated the SASA again:
> >>
> >>measure sasa 1.4 [atomselect top all]
> >>10272.072265625
> >>
> >>After rotating the system, the SASA was 11.6 A larger. Any idea why
> >>the result is not consistent?
> >>
> >>Thanks,
> >>
> >> Gianluca
> >>
> >>-----------------------------------------------------
> >>Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> >> +1 (206) 685 4435
> >> http://artemide.bioeng.washington.edu/
> >>
> >>Research Assistant Professor at the Department of Bioengineering
> >>at the University of Washington, Seattle WA U.S.A.
> >>-----------------------------------------------------
> >
> >--
> >NIH Center for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >http://www.ks.uiuc.edu/Research/vmd/
> >
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> ----------------------------------------------------- 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/