Probably because they set diffently the acceptor-donor cutoff and the acceptor-hydrogen-donor angle. Use from:

and set the cutoff and angle to the values you wish.


On 30 January 2012 16:34, Abhinav Verma <> wrote:

 I am trying to get the list of hbonds formed using Apply-find-polarcontacts. 

 I searched and found some scripts, but they never give me the same result as the one by default pymol. 

 Any ideas how I can get the hbonds as a list.



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Thomas Evangelidis

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Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece