Re: [PyMOL] test for bonded atom

[Thomas Holder]

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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Thomas Holder
PyMOL Developer
Schrödinger Contractor

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[PyMOL] test for bonded atom

[Krisztina Feher]

Hi,

I wonder if there is any way to list atoms an atom is bonded to? 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.

Thanks in advance,
Krisztina 
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