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

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 1 11:22:15 PDT 2019

Hi Thomas,
	Adding ions is in the “Addions” module.  Here’s some example code:

from Addions import initiateAddions
from chimera import openModels, replyobj
initiateAddions(openModels.list(), “Cl-“, “neutralize”, replyobj.status)

Now, obviously the above code will only neutralize a positive system since it is adding “Cl-“ ions.  Your script would probably need to sum up the total  charge of your system in order to know what kind of ion to add…


> On Mar 31, 2019, at 8:10 AM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> 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 <mailto: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 <mailto: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 <mailto: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 <mailto:tevang3 at gmail.com>
>> website: https://sites.google.com/site/thomasevangelidishomepage/ <https://sites.google.com/site/thomasevangelidishomepage/>
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