Re: [PyMOL] get_area algorithm and dot_density accuracy

Thank you for your reply. With regard to the algorithm used, do you
have any idea which algorithm is used in the Pymol calculations? DSSP
is likely to be using the rolling ball method.

Regards.

On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito
<emi...@gm...> wrote:
> Hi
> The accuracy of the calculation depends on the dot_density value (the
> amount of sampling done) with 1 being the lowest quality and 4 being
> the best quality. A dot_density value of 1 uses less computational
> resources (time) than a dot_density of 4 because of the amount of
> sampling performed to calculate the surface area.
>
> With respect to your question regarding the difference between PyMOL's
> get_area command and the SASA calculated bye DSSP, these differences
> in surface area could be the result of different atom radii being
> used, the inclusion of hydrogen atoms, or differences in the algorithm
> used to calculate the SASA. The speed differences could be the result
> of different algorithms and how they are implemented.
>
> You might want to check out FreeSASA ( http://freesasa.github.io ) to
> perform your SASA calculations.
>
> Emilio
>
> On Wed, Apr 26, 2017 at 11:49 PM, Ahmad Abdelzaher
> <und...@gm...> wrote:
>> I would appreciate any help regarding this.
>>
>> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
>> <und...@gm...> wrote:
>>> Hello,
>>>
>>> Does the get_area command use the rolling ball algorithm? Which
>>> dot_density corresponds to the best accuracy 1 or 4? Is there a reason
>>> why it consumes more time to compute sasa? Dssp takes significantly
>>> less time to do the calculations, however compared to Pymol
>>> dot_density of 3, the areas sometimes differ by 4,5,6,  squared
>>> angstroms!
>>>
>>> Any comment on that?
>>>
>>> Regards.
>>
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