On Tuesday 06 January 2004 20:06, Sanishvili, Ruslan wrote: > Is there a way to calculate and display H-bonds within a selected model > without going through the distance wizard? Selecting the pairs of atoms > manually via the distance wizard seems very inefficient and even > dangerous (too subjective for H-bond assignment).
1) The "dist" command will draw distance lines between all atoms of two different selections that are within a a specified cutoff distance from each other. A very rough approach for identifying potential hydrogen bonds would be something like dist (protein and elem n,o) , (ligand and elem n,o), 3.5 This will connect all nitrogen and oxygen atoms in objects "protein" and "ligand" that are within 3.5 A from each other. 2) A more thorough approach would be to use a program designed to identify hydrogen bonds using more complete criteria. The rTools for PyMOL (available at <http://www.rubor.de/bioinf/pymol_rubor.html> ) provide an interface to the HBExplore program at <http://www.imb-jena.de/www_bioc/hbx/hbx.html>. See the rTools documentation for more details. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
