Hi Krisztina,
I wonder if there is any way to list atoms an atom is bonded to?
Use the neighbor selection operator:
PyMOL select newsele, neighbor (othersele)
See also:
http://pymolwiki.org/index.php/Selection_Algebra
I would
like to list H bonded pairs but the available scritps (list_hbonds.py,
or polarpairs.py) only check for distance and angle between heteroatoms,
but not if any of them is actually connected to a hydrogen. As a result
two carbonyl atoms are listed too.
Have you also tried the distance command? It is very similar to
list_hbonds/polarpairs:
PyMOL distance hbonds, all, all, mode=2
There is no direct way to list these pairs, but you can use
get_raw_distances script from the PyMOLWiki:
http://pymolwiki.org/index.php/Get_raw_distances
Hope that helps.
Cheers,
Thomas
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PyMOL Developer
Schrödinger Contractor
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