From: Sampo Karkola (
Date: Wed Jan 02 2008 - 06:13:39 CST


I was wondering if it is possible to select atoms (or residues) from a
protein based on a ligand that is not part of the protein? For example,
I have a protein structure (as molecule 0) with an empty cavity and I
read in a docked ligand (as molecule 1) and I would like to select
protein residues in a 6 sphere around the ligand. If this is not
possible, is there a command to merge the ligand to the protein structure?

This subject might have been discussed recently on the list but I could
not find it in the archives.



Sampo Karkola
Doctoral student

Laboratory of Organic Chemistry
Department of Chemistry
POBox 55, FIN-00014
University of Helsinki

tel. +358 9 191 50369
fax. +358 9 191 50366