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 > <spel...@users.sourceforge.net <mailto: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 ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net