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 <teva...@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 <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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