It is in the directory from which you started coot (that is, if coot can
create and write to such a directory (if not it is in your home directory)).
Paul.
On 15/02/2024 23:51, Kim, Sun Kyung wrote:
Thank you Lucrezia for your informative reply!
You suggested I look into coot-molprobity output directory. Where can
I locate this directory?
Thank you.
Best,
‘Kate’ Sun Kyung Kim
*From: *Lucrezia Catapano <lucrezia.catap...@kcl.ac.uk>
*Date: *Friday, February 2, 2024 at 6:21 AM
*To: *Kim, Sun Kyung <kim...@llnl.gov>, COOT@JISCMAIL.AC.UK
<COOT@JISCMAIL.AC.UK>
*Subject: *Re: How does COOT determine protonation states
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
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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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