Hi Jared,


Thanks for your reply.  I was aware of the distance command (polar contacts).  The pseudo atom solution could work, but to be honest, I’d prefer a solution that would detect these interactions.


I’ve found InteractionDetector.py (https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/modules/ADT/AutoDockTools/InteractionDetector.py), and I’m wondering if this could be adapted to work with neat PyMOL.  Unfortunately, I don’t speak python L





From: Sampson, Jared [mailto:Jared.Sampson@nyumc.org]
Sent: Wednesday, August 13, 2014 3:07 PM
To: Markus Heller
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Show cation-pi/pi-pi interactions


Hi Markus - 


It’s already possible to highlight polar interactions using the `distance` command with mode=2.  http://www.pymolwiki.org/index.php/Distance


For pi-cation stacking, it might be useful to create pseudo atoms at the average position of the atoms in each charged group or ring in question (e.g. `pseudoatom ring_Y102, resi 102 and name CG+CD1+CD2+CE1+CE2+CZ`) and use them to create sensibly positioned distance dashes between them.





Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center


On Aug 13, 2014, at 4:59 PM, Markus Heller <mheller@cdrd.ca> wrote:


There's a thread in the PyMol Wiki (http://www.pymolwiki.org/index.php/Ideas) that mentions the possible implementation of functionality to highlight H-bonds, salt bridges, Pi-stacking, Pi-cations.  Has such a thing been implemented yet, and if not, what's the current status?

Thanks and Cheers

Markus Heller, Ph.D.
NMR Scientist
CDRD - The Centre for Drug Research and Development
2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147
Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller@cdrd.ca | www.cdrd.ca

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