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 Baumgartner <mpb21@pitt.edu> wrote:
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 on the ligand and notice that pymol added a hydrogen
almost along an existing bond to another ring.

I am running pymol on Ubuntu 13.04.

I'm not sure if this has been reported before and has been fixed already
in 1.6. I haven't gotten around to upgrading yet, but I am willing to.



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Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900