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 <jmsstarlight@gmail.com>
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 <speleo3@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
[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
<speleo3@users.sourceforge.net <mailto:speleo3@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