Re: [PyMOL] [EXTERNAL] Question about polymer selection criteria

Hi Ryan and Blaine,

In addition to the classification by residue identifiers, PyMOL looks for nucleic acid backbone atoms by name.

See:
https://github.com/schrodinger/pymol-open-source/blob/master/layer3/Selector.cpp#L1393
----------------------
        } else if (found_o3star && found_c3star && found_c4star && found_c5star
               && found_o5star && (found_o3_bond || found_p_bond)) {
          mask = cAtomFlag_polymer | cAtomFlag_nucleic;
----------------------

Hope that helps.

Cheers,
  Thomas


> On May 18, 2019, at 12:26 AM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> 
> Hi Ryan,
> 
> I think that the manual page for polymer will answer your question clearly
> 
> https://pymol.org/dokuwiki/doku.php?id=selection:polymer
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Kung, Ryan [rya...@ul...]
> Sent: Friday, May 17, 2019 4:46 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] Question about polymer selection criteria
> 
> Hello,
> 
> I have a question about how the pymol polymer.nucleic selection defines what is nucleic? Is there a list of atom names that are required? Does it have to actually be part of a polymer for the selection process to identify it? If someone can help me understand this, that would be great.
> 
> Thank you,
> Ryan Kung
> 
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.