VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 09 2015 - 16:33:37 CDT

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.
> ----------------------------------------------------- 

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