[PyMOL] Visualisation of protein-ligand interactions in pymol

[James S. <jms...@gm...>]

Dear PyMol Users!


I'm performing visualisation of the results of my MD simulation-
protein-ligand system in water.

1) I want to visualise individual water mollecules wich have moved to the
protein interiour during my MD run. How I could hide all solvent water and
visualise only those water wich are within defined cutoff distance from the
protein ?


2) I've compared electrostatic protein- ligand contacts by means of PyMol's
present- ligand sites option. As I've noticed the polar contacts are
visualised as the different object. It's very uncomfortable in case when I
want to compare protein-ligand interactions in two conformations of my
protein by means of GRID mode because the polar interactions from both
conformations as the different objects. So as the result I obtain 4 objects
( 2 of proteins +2 of polar contacts as the simple distances ) instead of 2
conformations with the polar distances. Is there any possible way to merge
polar interactions with the protein structures to one object ?


Thanks for help,

James S.