From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 09 2015 - 16:52:40 CDT

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.
-----------------------------------------------------