Re: [PyMOL] list of polar contacts

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 <te...@gm...>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 <abh...@gm...> 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 <te...@gm...>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 <abh...@gm...> 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
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>>> email: te...@bi...
>>>
>>>           te...@gm...
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>>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: te...@bi...
>
>           te...@gm...
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>