From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sat Apr 11 2015 - 15:16:39 CDT

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