Frank, PyMOL adds hydrogens based on the hybridization and formal charge of an atom...if you're not getting the right number of hydrogen, then you probably need to adjust either the valences of the bonds it participates in, or the formal charge.
A) To adjust valences: 1) enable "show valences" from the Display menu 2) put the mouse into editing mode 3) ctrl-right-click to pick a bond and then 4) Type Ctrl-W or select Cycle-Valence from the Build menu to cycle through the possible valences/ B) To change the formal charge of an atom: (first make sure no other atoms are picked -- click Unpick if necessary) Ctrl-middle-click to pick the atom Ctrl-K -> makes atom positive Ctrl-J -> makes atom negative Ctrl-U -> makes atom neutral C) To replace hydrogens on any atom: (first make sure no other atoms are picked -- click Unpick if necessary) Ctrl-middle-click to pick the atom Ctrl-R or select Fill Hydrogens from the build menu to rebuild hydrogens on that atom. "remove hydro" can be used to remove all atoms h_add will put them back. Note that PyMOL doesn't yet know how to properly name hydrogens on standard protein & dna residues. That will come in time. Cheers, Warren > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > S. Frank Yan > Sent: Wednesday, April 07, 2004 12:10 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] add hydrogens using different hybridization > > Hi, > > I was wondering if there is a way to add hydrogens to a > selected atom based on different hybridization, e.g., sp2, > sp3, etc., in which way different number of hydrogens will be > added with the corresponding geometry. > > Thanks, > Frank > > > __________________________________ > Do you Yahoo!? > Yahoo! Small Business $15K Web Design Giveaway > http://promotions.yahoo.com/design_giveaway/ > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
