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 <abhinav1...@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 <teva...@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 <abhinav1...@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: tev...@bioacademy.gr
>>
>> teva...@gmail.com
>>
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>>
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--
======================================================================
Thomas Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece
email: tev...@bioacademy.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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