João, Thanks for being patient on this. I just moved to a big city and am still getting settled.
PyMOL does indeed need four passes. It fills in hydrogens one at a time, positioning them in idealized locations based upon the structure of the neighbor to which it will be bound. If it's adding hydrogens to a planar, linear or tetrahedral arrangement, PyMOL places the atoms in different -- idealized -- locations. PyMOL finds the open valence vector for and fills positions according to that. On Tue, Jun 22, 2010 at 3:42 PM, João Rodrigues <anar...@gmail.com> wrote: > Hello all, > > I've been looking at Pymol's code for sometime time now and yet the > algorithm for addition of hydrogen atoms to molecules in Pymol is not clear > to me.. > > I've traced the h_add function to OMOP_AddHydrogens in layer2/Executive.c: > > op.code = OMOP_AddHydrogens; /* 4 passes completes the job */ > > I'd argue this "4 passes to complete the job" requirement is related with > the algorithm in chempy/place.py that iterates over a "need" list of lists. > > need = [ [], [], [], [] ] > > This list of lists hold info for heavy atoms that lack 1, 2, 3, or 4 atoms. > > This seems quite logical. But then the H atoms added have names like H01, > H02, etc, when they were correctly identified in chempy/proteins.py and have > their names in protein_amber.py and protein_residues.py. > > My main questions are: are there different treatments for proteins when it > comes to H-addition? How are H-s added to say, Methane? (given a single C). > > Best! > > João [...] Rodrigues > @ http://doeidoei.wordpress.org > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > 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 ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ 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
