Thanks Thomas!

I've already tried use this command.

I want just ask about Hbond representation between 2 selected regions.

E.g I want to represent Hbonds beetween 2 helices

Firstly I've added donor Hydrogens

H_add donors

and than

distance 3sn6 and resi 197-220, 3sn6 and resi 275-298, cutoff=4, mode=2
where first selection is the 1st helix and second selection is another helix of my protein.

I've noticed that in some cases there are errors in the h-bond network. How I could fix it ?


2012/1/24 Thomas Holder <>
Hi James,

use the distance command:

For the potential h-bonds, use it with mode=2.


On 01/24/2012 05:15 PM, James Starlight wrote:
Dear PyMol Users!

In the PyMol Wizard I've found very userful option called distance
measurements beyween selected atoms.

I wounder to know how I could realize such operation via PyMol console
in the simplest manner.

My current task consist of making different point mutations and
subsiquent quick measurement of the new distance between new mutated
residue and some other native residue.

In addition I'd like to measure potential H-bond distance between above
residues (polar contacts between electronegative groups) as well as
tight packing forces ( distance between non-polar residues).

Is there any simplest method for that purpose ?



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