Re: [PyMOL] Polar interactions within selection

[James S. <jms...@gm...>]

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 <
sp...@us...> 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
>> <sp...@us... <mailto:speleo3@users.**sourceforge.net<sp...@us...>
>> >>
>>
>> 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
>