By the way how I have the slightly another task- I want to see all VDV
contacts surrounded selected residues. What should I make changes in the
Thomas's script for that ?
e.g firstly I've defined another residues in that case I have only one type
of residues- all hydrophobic residues. But what
Thanks, Thomas!
Your script works fine. I've tested in one pdb structure and it finds all
polar and salt-bridges perfectly.
As I've understood this script also is usefull for examination of the
ensemble of pdb structures in NMR-like format ( each pdb structure as the
individual state in pymol)
Hi James,
maybe something like this could help. It finds contacts between charged
sidechains and prints the number of contacts in each state (requires
get_raw_distances from [1] or [2]).
# region of interest
select roi, chain A
# charged
Dear PyMol users!
I'm analysing polar interactions occured during MD simulation of my
protein. In particular I have PDB file obtained from such trajectory where
I'd like to check new polar contacts ( salt bridges first of all) within
selection region. I've tried to select specified region and