From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 09 2015 - 21:06:27 CDT

Hi,
  At present the "measure sasa" SASA feature in VMD is simplistic and it
won't do things like you describe in a single-pass calculation.

There is another experimental sasa variant in VMD 1.9.2 called
"measure sasalist" that accepts a list of atom selections and it
can compute sasa values for multiple selections at once using
a parallel algorithm. You might try that if you really don't want
to run other tools in your scripts.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 09, 2015 at 03:34:43PM -0700, Gianluca Interlandi wrote:
> Thanks John,
>
> I will try out nanoshaper in the future.
>
> Another question concerning "measure sasa". Is there a way to make
> it efficient? For example, I would like to calculate the SASA of all
> side chains individually, but for that I would have to run "measure
> sasa" multiple times. Is there a way to calculate the SASA for all
> atoms individually in one single shot and then sum the contributions
> for each side chain? I know that I could use DSSP for that, but I'm
> using it as part of a TCL script.
>
> Thanks,
>
> Gianluca
>
> On Thu, 9 Apr 2015, John Stone wrote:
>
> >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/
> >
>
> -----------------------------------------------------
> 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/