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

[Jared S. <jar...@co...>]

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
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe