Re: [PyMOL] Seeing more H-bonds than expected

Thank you Jared for the detailed explanation!

Neena

On Tue, 9 Apr 2019 at 12:35, Jared Sampson <jar...@co...>
wrote:

> Hi Neena -
>
> PyMOL shows all the potential H-bonds, but not all of them will be formed
> at all times. Any single proton can only participate in one H-bond at a
> time, but remember a crystal structure is an average structure based on the
> ensemble of states present in the protein crystal (or on the EM grid for
> cryo-EM structures).  It's ok to have "too many" polar contacts...it just
> means the atoms have options for where to interact.
>
> Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds.  See
> perhaps McDonald & Thornton, JMB (1994)
> https://doi.org/10.1006/jmbi.1994.1334 for a more detailed discussion.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On April 4, 2019 at 11:25:17 PM, Neena Susan Eappen (
> nee...@gm...) wrote:
>
> Hello PyMOL users,
>
> Hydrogen bond finder on Pymol sometimes gave me unexpected observations
> like:
> more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on.
> This is even after setting H-bond center cutoff to 3.0 A. Any insight would
> be appreciated.
>
> Thank you for sharing your knowledge,
> Neena
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