Re: [PyMOL] Polar interactions within selection

2012-06-07 Thread James Starlight
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

Re: [PyMOL] Polar interactions within selection

2012-04-17 Thread James Starlight
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)

Re: [PyMOL] Polar interactions within selection

2012-04-16 Thread Thomas Holder
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

[PyMOL] Polar interactions within selection

2012-04-04 Thread James Starlight
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