[Chimera-users] create automatically all alternative protonation states of protein

[Thomas Evangelidis]

OK, i found an older post about how to run DockPred from a script. But i
cannot find how to add ions in Python. Is there any way to neutralize the
system in Python without adding waters?

Dne pá 29. 3. 2019 5:28 PM uživatel Thomas Evangelidis <tevang3 at gmail.com>
napsal:

> Hi Eric,
>
> Thanks for the hints, i programmed it to consider also the atom that
> receives the proton. To make the code complete, namely to generate
> structures ready for docking or MD, is it possible to do the following in
> python?
>
> * if alternate locations keep only highest occupancy.
> * convert modified residues to standard residues.
> * replace incomplete sidechains.
>
>
> Basically what DockPred does but in python.
>
> Best,
> Thomas
>
> Dne čt 28. 3. 2019 6:10 PM uživatel Eric Pettersen <pett at cgl.ucsf.edu>
> napsal:
>
>> Hi Thomas,
>> The same atom name will always receive the proton (as noted on the addh
>> help page).  Your two options are to swap the atom names, or use the
>> “rotate” command to rotate the appropriate bond by 180°.  For example, to
>> swap the names of OE1 and OE2 in GLU 102 of chain A:
>>
>> setattr a name XX :102.A at OE1
>> setattr a name OE1 :102.A at OE2
>> setattr a name OE2 :102.A at XX
>>
>> Similarly, to rotate the CG-CD bond of that residue:
>>
>> rotation 1 :102.A at CD,CG
>> rotation 1 180
>> ~rotation 1
>>
>> —Eric
>>
>> On Mar 28, 2019, at 7:11 AM, Thomas Evangelidis <tevang3 at gmail.com>
>> wrote:
>>
>> Hello again!
>>
>> @Jaime
>> Thanks, PyChimera worked great!
>>
>> @Eric
>> I wrote a script and posted it to a new thread to avoid confusion with
>> this one. However, I just spotted a flaw. Is it possible to control to
>> which oxygen of the carboxylate the proton is added? Ideally, I want to get
>> both alternative protonations. If not then to flip the resulting carboxylic
>> group by 180 degrees. Could you give me some hints, please?
>>
>> best,
>> Thomas
>>
>>
>> --
>>
>> ======================================================================
>>
>> Dr Thomas Evangelidis
>>
>> Research Scientist
>>
>> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech
>> Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
>> Prague, Czech Republic
>>   &
>> CEITEC - Central European Institute of Technology
>> <https://www.ceitec.eu/>
>> Brno, Czech Republic
>>
>> email: tevang3 at gmail.com
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
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>>
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