Dear Kate,

Just to clear up some potential confusion and contradiction between Lucrezia's 
and my answer. Coot has various ways in generating hydrogens, internally using 
the dictionaries as Lucrezia nicely mentioned and explained, and externally 
using e.g. refmac or reduce (as I mentioned earlier). In the 0.9 series of Coot 
which you are using, the Validation function Probe clashes will use reduce. You 
can see this in the command line output which will state something about reduce 
(followed by probe).

HTH,

B

***************************************************

Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent

Teaching Unit/Biomedicum D9
Dept. of Medical Biochemistry and Biophysics (MBB) |
Karolinska Institutet
SE-171 77 Stockholm
Sweden
+46 8 52487055
bernhard.lohk...@ki.se | ki.se

> -----Original Message-----
> From: Mailing list for users of COOT Crystallographic Software
> <COOT@JISCMAIL.AC.UK> On Behalf Of Lucrezia Catapano
> Sent: Friday, February 2, 2024 3:21 PM
> To: COOT@JISCMAIL.AC.UK
> Subject: Re: How does COOT determine protonation states
>
>       You don't often get email from 0000ade43f7741e4-dmarc-
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>
> Dear Kate,
>
>
>
> Coot adds hydrogen atoms according to the dictionary. If you want to change
> the protonation of a ligand, you'd do that by modifying the actual monomer
> dictionary. We typically use Acedrg to generate dictionaries.
>
> For example, in the case of a ASP residue, the modification which describes
> the addition of the proton, encapsulates all the local changes (bond order,
> angles etc.) of the monomer, providing the (probably) expected geometry.
>
>
>
> Look in your coot-molprobity output directory. These files are used by
> Reduce to protonate ligands - Coot converts the (Acedrg, or whatever else)
> dictionary you have given it, to these files of connection records.
>
>
>
> Regards,
>
> Lucrezia
>
>
>
>
>
> From: Mailing list for users of COOT Crystallographic Software
> <COOT@JISCMAIL.AC.UK> on behalf of Kim, Sun Kyung <0000bc51fd01f63f-
> dmarc-requ...@jiscmail.ac.uk>
> Date: Tuesday, 30 January 2024 at 00:36
> To: COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
> Subject: How does COOT determine protonation states
>
>       Some people who received this message don't often get email from
> 0000bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk. Learn why this is
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>
>
> Hello,
>
>
>
> I’m using the Coot 0.9.8.91 EL. I am working jointly with a computational
> team who are doing simulations on our PDB model. I’ve added hydrogens to
> my model using Coot’s Validate -> Probe clashes function. The computational
> team asks, when COOT adds protons using the probe clashes function, how
> does it assign protonation states to residues? Is it using something
> sophisticated that we can trust for our computational simulations or should
> the computational scientists use their own methods for determining
> protonation states?
>
>
>
> Thank you for your time answering this question, much appreciated!
>
>
>
> Best,
>
> ‘Kate’ Sun Kyung Kim
>
>
>
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