Re: [PyMOL] Molecular surface area
Hi Andreas, dot_solvent=0 is solvent excluded surface, also known as molecular surface or Connolly surface. PyMOL approximates it numerically by sampling points on the surface See: https://pymolwiki.org/index.php/Get_Area#Settings Cheers, Thomas > On May 19, 2019, at 10:08 PM, Andreas Tosstorff > wrote: > > Hi all, > > I am looking for the method by which the get_area command calculates the > molecular surface area when dot_solvent=0. > It is described for SASA in the mailing list but I could not find it for the > default method. > Thanks a lot for your help! > Andreas > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] 3D viewing issue
I had an old PC that a person was using pyMol and displaying 3D. I needed to replace the hard drive and now I can't seem to get pyMol to display 3D. I have the following hardware (That of course used to work just fine) APG6000 Active Glasses & IR Emitter System NuVision 60GX-T50 60GX-G5 (IR emitter) Quadro 3700 graphics card. DepthQ WXGA projector This was running XP. So I installed XP, latest Nvidia drivers and the latest 32bit version of pyMol. The refresh rate on the projector is 120Hz the IR emitter is hooked up to the little DIN connector on the video board. I set Stereo Enable to on. When I start pyMol in Quad Buffered 3D, it says "Yep, I see your card 3D is OK" and when I choose to display in Quad Buffered Stereo it looks to the naked eye that there are the two images. I have checked the IR is emitting (via phone camera) and have tried multiple glasses to rule out dead battery in them. I imagine that I'm missing some silly setting or something. (I have also tried this with Windows 10 and the latest version of pyMol with same results). I know this is an old setup, but it was working just fine before the rebuild. I have no idea what I must be missing. Any suggestions are welcome. Thanks. Jim Earnshaw Senior Computer Specialist Department of Chemistry University of Washington 206-616-4967 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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)
> 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 [ryan.k...@uleth.ca]
> Sent: Friday, May 17, 2019 4:46 PM
> To: pymol-users@lists.sourceforge.net
> 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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> Unsubscribe:
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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