VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Apr 11 2015 - 15:20:01 CDT

Gianluca,
  The code doesn't currently cope with periodicity, but this could
be dealt with by replicating periodic images. In principle it should
not be difficult to modify the code to support PBC handling, but
it isn't there yet.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 11, 2015 at 01:16:39PM -0700, Gianluca Interlandi wrote:
> Dear John,
>
> Hopefully, my last question about "measure sasa". Is there a way to
> take into account the periodicity? For example, I have a protein on
> a surface and in some instances it might move to the edges, but I
> still need to take into account that it is in contact with the image
> of the surface.
>
> Thanks!
>
> Gianluca
>
> On Thu, 9 Apr 2015, John Stone wrote:
>
> >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/
> >
>
> -----------------------------------------------------
> 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/