Re: [PyMOL] Algorithm used to retrieve ss ?

[Thomas Holder]

Hi Hélène,

It's a custom algorithm developed by Warren DeLano. Some of the details are 
discussed in this post:
https://sourceforge.net/p/pymol/mailman/message/7561993/

The implementation is in SelectorAssignSS in layer3/Selector.cpp:
https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer3/Selector.cpp#l1885

Hope that helps.

Cheers,
  Thomas

> On Apr 4, 2018, at 11:59 AM, Hélène Kabbech  wrote:
> 
> Dear pymol users,
> 
> For a project based on proteins secondary structures (ss), I need to know 
> which algorithm/program does PyMol use to retrieve secondary structures from 
> a pdb file (when the ss datas are not display in the file).
> 
> I retrieved ss using dssp program, and for some pdb files, it shows strands 
> or helix which are considered as loop by PyMol I guess.
> 
> Thank you for your help.
> 
> Best regards,
> Hélène

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Algorithm used to retrieve ss ?

[Hélène Kabbech]

Dear pymol users,

For a project based on proteins secondary structures (ss), I need to know
which algorithm/program does PyMol use to retrieve secondary structures
from a pdb file (when the ss datas are not display in the file).

I retrieved ss using dssp program, and for some pdb files, it shows strands
or helix which are considered as loop by PyMol I guess.

Thank you for your help.

Best regards,
Hélène
--
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