By the way
in some papers I've seen 2D schematic diagrams of the protein-ligand interactions.
The exapmle of such maps could be found here http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-gr4.jpg
Could you tell me examples of software wich could produce such maps?
Thomas, thanks this works perfect.
Jason, I've tested this script on my system ( this is the membrane protein inserted in the bilayer surrounded by two water layers ( up and down ). During simulation individual water mollecules move into the protein interiour ( in that case protein like a water pore althought it's the receptor ) so I want to visualise only that buried water.
I've tried to do it via find_buried_waters script both via ASA as well as in case when I've used small cutoffs ( 0.1) but the script selected too many waters ( e.g virtually all waters from up and down layers have been selected ). How I could specify this selection more carefully ?
find_buried_waters 1, 0.1
James2012/6/12 Thomas Holder <email@example.com>
sorry, not "group mode" but "grid mode" of course.This will show them in the same slot in group mode.
MPI for Developmental Biology