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 exaclty cutt-offs and addition python modules should I use?


2012/4/17 James Starlight <>
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) isn't it?

So now I must find a way to save my trajectories in this NMR-like pattern by means of vmd software. I have found only possibility to save individual snapshots as the individual pdb files or as the set pdb in one pdb in one state ( i think this is not very usefull). Do you know how any python modules for working with and extracting snapshots from big trr files from gromacs runs ?

Thanks again


16 апреля 2012 г. 19:18 пользователь Thomas Holder <> написал:

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 residues
select positive, resn ARG+LYS and not name N+O
select negative, resn GLU+ASP and not name N+O

# increase cutoff
set h_bond_cutoff_center, 5.0
set h_bond_cutoff_edge , 5.0

# find polar contacts
delete saltbridges
distance saltbridges, roi and negative, roi and positive, mode=2
hide label

# count contacts in each state
except NameError:
   from psico.querying import get_raw_distances

for state in range(1, cmd.count_states()+1):
   sb = get_raw_distances('saltbridges', state)
   print ' %2d charged contacts in state %d' % (len(sb), state)
python end



On 04/16/2012 03:22 PM, James Starlight wrote:
Hi Thomas!

Yes I'd like find possible way for quick examining of the polar
interactions ( nor only h-bonds but mainly salt-bridges) within
selection. As the consequence I'd like to examine the ensemble of the
pdb fies obtained as the different snapshots from MD trajectory for the
evolution of the new salt-bridges occuring during simulation.


16 апреля 2012 г. 15:58 пользователь Thomas Holder
< <>>


   Hi James,

   I just noticed that this question is without any answer on the
   mailing list. Do you still need help on this topic?


   On 04/04/2012 09:26 AM, James Starlight wrote:

       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 use
       Find polar contact- > within selection as well as other options from
       this context meny but results was blank and I have not seen any
       contacts despite some charged residues were presented in the
       interface positions in the selected region.

       IS there any else way to study dynamics of the salt-bridges
       based on the selected regions in the snapshots ?

       Thanks for help,


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