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.


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