There are many ways you can use PyMOL for the analysis of protein-ligand interactions. It would be helpful to state what type of interactions you are particularly interested in. However, the most obvious one is to analyze hydrogen-bond formation between the complex. It is pretty well explained in the PyMOL Wiki ( http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts ), which is a great resource anyway. Then I would look at obvious signs of planar stacking of aromatic rings. In addition steric clashes can be analyzed quite well using the show_bumps command in PyMOL ( http://www.pymolwiki.org/index.php/Show_bumps ). Hope this helps you a little for a start.
Thanks Peter and Sebastian for your wonderful suggestions. I will definitely act accordingly.
The easiest way to observe any receptor-ligand interaction in PyMOL is!
(1) Load your complex.
(2) Hide water etc if any for visibility enhancement...
(3) Click the action button (A) and scroll down to presets that will walk you through to another list where you will find "ligand sites".
(4) Select ligand sites and it will open into another list, there click on the option "cartoon".
The whole complex will turn rainbow and you can rotate the structure, zoom in and out to explore the interactions.
Good luck
Neeraj kumar Patel
Here I put some useful commands: https://github.com/mtplr/pyMol-cookbook
Hi,
You can also visualize the interactions using online PLIP tool.
1) Google PLIP, https://projects.biotec.tu-dresden.de/plip-web/plip
2) Upload your best conformation PDB file.
3) Run, Analyze.
Best,
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