Ooops, got overzealous with button pushing and that email went out before I was ready. Continuing...
Another point: if the position of the hydrogen to add is ambiguous, PyMOL will randomly choose a position. (You can see this by creating a methane group from the builder, removing all hydrogens, and then h_adding them back. Remove/add them a few times to the lone carbon to see the effect of the randomized placement.) Cheers, -- Jason On Thu, Jul 1, 2010 at 10:40 AM, Jason Vertrees <jason.vertr...@schrodinger.com> wrote: > 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 > -- 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
