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
python
try:
get_raw_distances
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
--------------------------------------------------
[1] http://pymolwiki.org/index.php/Get_raw_distances
[2] http://pymolwiki.org/index.php/Psico
Cheers,
Thomas
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.
>
> James
>
> 16 апреля 2012 г. 15:58 пользователь Thomas Holder
> <[email protected] <mailto:[email protected]>>
> написал:
>
> Hi James,
>
> I just noticed that this question is without any answer on the
> mailing list. Do you still need help on this topic?
>
> Cheers,
> Thomas
>
>
> 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
> polar
> contacts despite some charged residues were presented in the
> adjacent
> interface positions in the selected region.
>
> IS there any else way to study dynamics of the salt-bridges
> formation
> based on the selected regions in the snapshots ?
>
> Thanks for help,
>
> James
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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