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
James
16 апреля 2012 г. 19:18 пользователь Thomas Holder <
spel...@users.sourceforge.net> 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
> 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<http://pymolwiki.org/index.php/Get_raw_distances>
> [2]
> http://pymolwiki.org/index.**php/Psico<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
>> <spel...@users.sourceforge.net
>> <mailto:speleo3@users.**sourceforge.net<spel...@users.sourceforge.net>
>> >>
>>
>> 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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