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 <mp...@pitt.edu> wrote:
> 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 on the ligand and notice that pymol added a hydrogen
> almost along an existing bond to another ring.
>
> I am running pymol 1.5.0.1 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.
>
> Thanks,
> Matt
>
> --
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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