Hi,
I may have found a bug in the way pymol interprets connectivity of
atoms. I noticed this in one pdb structure that I am working with 1RV1.
Steps to reproduce:
fetch 1RV1
#extract one of the ligands to it's own object
extract 'lig', /1RV1//A/110
#add hydrogens
h_add lig
Now look at atom C2
Just adding that N1, C2, and N3 in that ring are all sp2 hybridized. So the
H on the adjacent N is also in the wrong place.
Q: How is PyMOL determining ligand atom hybridization, by the way? Not
using the ligand CIF file at PDB, I guess?
Bob Hanson
On Fri, Jun 7, 2013 at 10:51 AM, Matthew
