From: Sanishvili, Ruslan <rsanishvili@an...> - 2004-01-06 19:07:05
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).
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT, Bld. 436, D007
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439
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.
Department of Ultrastructure
Vrije Universiteit Brussel