VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 09 2015 - 17:34:43 CDT

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