Hi Merlin - 

Try limiting the distances shown to those between atoms in specific selections using the `distance` command.  For example, to show H-bonds to solvent, disable the “my_obj_pol_conts” object created by the technical preset and use the command:

distance my_dist, my_obj and not solvent, my_obj and solvent, cutoff=3.5

Make sure to specify a cutoff or you’ll get every pair of polar atoms between your selections.

Hope that helps.

Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 27, 2014, at 3:33 AM, 天元 <422294399@qq.com> wrote:

Dear PyMol users!


I'm analysing polar contacts by "preset:technical". I got so many yellow bar measurements that I can't count the number. 

IS there any else way to count the number of all polar contacts ?

Thanks for help,


Merlin
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