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?
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 ?
James16 апреля 2012 г. 19:18 пользователь Thomas Holder <firstname.lastname@example.org> написал:
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  or ).
# 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
distance saltbridges, roi and negative, roi and positive, mode=2
# count contacts in each state
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)
On 04/16/2012 03:22 PM, James Starlight wrote:
Hi Thomas!<email@example.com <mailto:firstname.lastname@example.org>>
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
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
within selection region. I've tried to select specified region
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,
MPI for Developmental Biology