Hi Mitch, PyMOL adds hydrogens using C-code (layer2/ObjectMolecule.c:ObjectMoleculeAddSeleHydrogens). The code hasn't been validated (even though it does seem to work well).
PyMOL's naming convention for this is pretty simple it just names them H0X where X is the numbered pass in which PyMOL placed that hydrogen. For example, if you have just a carbon and want to add hydrogens to it, then PyMOL will create H01, H02, H03 and H04. I'm working on some other code that requires IUPAC naming, so I'll keep this in mind, too. There is probably a quick way to do it using chempy, but I haven't looked into that yet. Cheers, -- Jason On Mon, Oct 11, 2010 at 7:02 PM, Mitchell Jon Stanton-Cook <mitchell.stantonc...@uqconnect.edu.au> wrote: > Hello all, > > I was wondering if anyone could shed any light on the H0X nomenclature > applied when using the h_add. > > Ideally it would be nice to get the output protonated file in the BMRB > nomenclature as per (IUPAC/IUB Biochemistry 9, 3471-3479 [1970]). > > I have had a look at /usr/share/pyshared/chempy/protein.py (def > add_hydrogens) but nothing obvious stands out. > > The contents of protein_residues.py and amber_99.py etc. seem to suggest > that it indeed possible to write a more standard nomenclature. > > I just need a little help/direction. > > > Regards > > Mitch > > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ 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
