pymol-users

[PyMOL] Polar interactions within selection

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

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

Re: [PyMOL] Polar interactions within selection

[Thomas H. <sp...@us...>]

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
> <sp...@us... <mailto: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

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
>

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
>>
>
>