Hi thanks,

 still it is not the same.. But thanks.. 
 I wish Jason can reply if there is any way to get the list from the apply command.

thanks,
Abhi

On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis <tevang3@gmail.com> wrote:
I think you can reproduce the results from "apply->find->polar contacts" option with the PyMOL built-in "distance" command. E.g.
distance hbonds, all, all, 3.2, mode=2

The problem is that you cannot set the A-H-D angle which is important for the definition of the H-bond.



On 30 January 2012 18:45, Abhinav Verma <abhinav1205@gmail.com> wrote:
Thanks Thomas, 

 I have been here and my problem is that I could not reproduce the results of default pymol behaviour. I just need to either reproduce 100% the pymol default behaviour or to just get a list of what is painted in the window. It should be possible I guess.

 Do you have more ideas?




On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis <tevang3@gmail.com> wrote:
Probably because they set diffently the acceptor-donor cutoff and the acceptor-hydrogen-donor angle. Use list_hbonds.py from:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

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

Thomas



On 30 January 2012 16:34, Abhinav Verma <abhinav1205@gmail.com> wrote:
Hi,

 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.

Thanks,

Abhinav

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Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang@bioacademy.gr

          tevang3@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/




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Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang@bioacademy.gr

          tevang3@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/