Re: [PyMOL] get_area algorithm and dot_density accuracy

[Emilio X. E. <emi...@gm...>]

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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