Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

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

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 <sp...@us...>

> 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
>