[PyMOL] Distance measurement between atom groups

[James Starlight]

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 ?

Thanks,

James

[Thomas Holder]

Hi James,

use the distance command:
http://pymolwiki.org/index.php/Distance

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

Cheers,
Thomas

Post by James Starlight
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 ?
Thanks,
James

[James Starlight]

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 ?

James

Post by Thomas Holder
Hi James,
http://pymolwiki.org/index.**php/Distance<http://pymolwiki.org/index.php/Distance>
For the potential h-bonds, use it with mode=2.
Cheers,
Thomas

Post by James Starlight
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 ?
Thanks,
James

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