Re: [PyMOL] get_area algorithm and dot_density accuracy

[Emilio Xavier Esposito]

Hi
I am not sure which method is being used by PyMOL but because the
algorithm uses a dot density term it is likely the Shrake & Rupley
algorithm also known as the rolling ball method. You should read the
FreeSASA article (freely available
https://f1000research.com/articles/5-189/v1 ). The author provides a
really nice description of SASA calculations along with precision and
speed analysis.

Emilio

On Thu, Apr 27, 2017 at 7:38 AM, Ahmad Abdelzaher
 wrote:
> 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
>  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
>>  wrote:
>>> I would appreciate any help regarding this.
>>>
>>> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
>>>  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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Re: [PyMOL] get_area algorithm and dot_density accuracy

[Ahmad Abdelzaher]

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
 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
>  wrote:
>> I would appreciate any help regarding this.
>>
>> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
>>  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.
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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Re: [PyMOL] get_area algorithm and dot_density accuracy

[Emilio Xavier Esposito]

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
 wrote:
> I would appreciate any help regarding this.
>
> On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
>  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.
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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Re: [PyMOL] get_area algorithm and dot_density accuracy

[Ahmad Abdelzaher]

I would appreciate any help regarding this.

On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher
 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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