Re: [PyMOL] Polar interactions within selection

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

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?


James



2012/4/17 James Starlight <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
>>
>
>