RE: [PyMOL] add hydrogens using different hybridization

[Warren D. <wa...@de...>]

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: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> S. Frank Yan
> Sent: Wednesday, April 07, 2004 12:10 PM
> To: pym...@li...
> 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
> 
> 
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