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?


Thanks

James

2012/6/15 James Starlight <jmsstarlight@gmail.com>
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


James


2012/6/12 Thomas Holder <speleo3@users.sourceforge.net>
This will show them in the same slot in group mode.

sorry, not "group mode" but "grid mode" of course.


--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen