VMD-L Mailing List

From: Nuno Sousa Cerqueira (nscerque_at_fc.up.pt)
Date: Fri Jun 18 2010 - 15:20:23 CDT

Hello,

I have just come from a summer school on GPU computing.
I was wondering if the SASA algorithm would be a nice code to
implement in CUDA?
Is there any work going in this direction?

Regards,

Nuno

Begin forwarded message:

> From: John Stone <johns_at_ks.uiuc.edu>
> Date: June 18, 2010 8:22:19 PM GMT+01:00
> To: Edward Lyman <edward.lyman_at_gmail.com>
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: -samples flag of measure sasa
>
>
> Edward,
> Yes, the 'atom' sphere sizes are the atom's radius plus the probe
> radius,
> as you can see on line 1132 of the code there. Yes, 500 samples are
> used
> by default. The code doesn't treat any atom type specially, it
> applies
> the same rules to all. All of the radii are specific to each atom, so
> it just uses what it's given. You can manipulate how it behaves by
> changing the radii of your atoms, or by selecting or not selecting
> some
> atoms.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 18, 2010 at 01:15:10PM -0600, Edward Lyman wrote:
>> Thanks very much, that is useful information: area/point =
>> (surface area
>> of the atom)/(number of randomly sampled points).
>>
>> the surface are of the 'atom' is actually the area of the sphere
>> with a
>> radius = (atom radius + probe radius), right?
>>
>> It looks from the code that 500 random points are used...is that
>> correct?
>>
>> So...*IF* I could assume that every atom considered in the SASA
>> calculation has the same radius, I would know the area/point, and
>> I could
>> easily calculate the area for each separate patch.
>>
>> one last question: are the H's and the C's considered seperately
>> for the
>> purpose of the SASA calc? or do you just puff out the radius of the
>> carbons a little bit and save some calculation time?
>>
>> Thanks very much for the help.
>> Ed
>>
>> On Fri, Jun 18, 2010 at 12:10 PM, John Stone <johns_at_ks.uiuc.edu>
>> wrote:
>>
>> Hi,
>> The -samples flag controls how many random sample points are
>> used
>> to estimate the surface area for each atom. The points are
>> distributed
>> randomly over the sphere, and the area is estimated by
>> multiplying the
>> fraction of samples that are exposed by the surface area of the
>> sphere
>> for the atom under consideration. When you retrieve the actual
>> list of
>> sample points, you are getting the points that passed the solvent
>> accessibility test for the combination of selection and/or
>> restricted
>> selection you provided. Does that answer your question?
>>
>> You can see the source code that implements the calculation in
>> the
>> measure_sasa() routine here:
>> http://www.ks.uiuc.edu/Research/vmd/doxygen/Measure_8C-source.html#l01058
>>
>> (that URL will change with time, but it's good for the short-
>> term)
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>> On Thu, Jun 17, 2010 at 10:47:34AM -0600, Edward Lyman wrote:
>>> Hi all,
>>>
>>> I am looking for an explanation of the -samples flag for measure
>> sasa
>>> (somehow it has been omitted from the manual). I guess it is
>>> simply
>> the
>>> density of points that is used to sample the surface, but I would
>> like to
>>> know what is the default value, and what the value means. For
>> instance,
>>> does each point represent a (roughly) constant area? Or is each
>> point a
>>> vertex in a more complicated (eg, Delaunay) triangulation, and so
>> could
>>> represent a wide range of areas?
>>>
>>> My interest stems from the following problem: I have used "measure
>> sasa"
>>> to identify several distinct patches of solvent accessible
>>> residues
>> on the
>>> surface of a protein. I can store those points, and then post
>> process them
>>> using a simple (breadth-first) search algorithm to automate the
>> process of
>>> distinguishing different patches. Now I want to know the area of
>> each
>>> patch. If each vertex represents a constant area...problem solved.
>> But if
>>> the surface is more complicated...the problem becomes considerably
>>> trickier, and I then have to recover the (nonoverlapping)
>>> triangles
>> in
>>> each patch and add up their areas.
>>>
>>> Thx,
>>> Ed
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078

Phd, Nuno M. F. Sousa A. Cerqueira
Assistant Researcher
------------------------------------------------------------
Chemistry Department, Faculty of Sciences
University of Porto
Rua do Campo Alegre, s/n
4169-007 Porto - Portugal

Tel: +351 220402501
Fax: +351 220 402 009
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http://www.fc.up.pt/pessoas/nscerque