Hello Kate,
Attached is an example conn file: it is in a folder called
coot-molprobity and has the required format for input to Reduce.
> In COOT, does REDUCE take into account pH and local changes in pKa of
atoms when determining protonation states?
In SMILES-speak: NCC(=O)[OH] and [NH3+]CC(=O)[O-] are two entirely
different molecules with different residue names. The bond orders,
charges, bond lengths and so on are defined by the restraints generator.
Coot and Reduce are only doing what they are told to do.
> In COOT, when REDUCE adds hydrogens, does it move any of the non-H
atoms too to optimize geometry?
Reduce does not move the non-hydrogen atoms (unless you ask it to do HQN
flips). This is true whether or not it is launched from Coot.
> In COOT, does REDUCE automatically flip ASN and GLN and HIS
sidechains to optimize H-bonding?
HQN flips are on by default, IIRC.
This is a discussion about ancient (10 years old) code. More recent is
the use of Acedrg and Coot's internal hydrogen atom addition method. If
you want to have a discussion about protonation and tautomerisation
manipulation then we should be talking about that in the context of
Acedrg (and Grade2 if you're on the cutting edge of Coot progress).
Regards,
Paul.
On 20/02/2024 21:09, Kim, Sun Kyung wrote:
Thank you Paul, for your reply! I was not able to locate the exact
dictionary but I think I was searching probably in the right folder…
what is the file type I should be looking for?
More pressing questions for me are about REDUCE that’s used in COOT:
1. In COOT, does REDUCE take into account pH and local changes in pKa
of atoms when determining protonation states? Since I don’t input
the pH value anywhere, I’m assuming that it probably just assumes
physiological pH of 7.4 when it calculates protonation states, am
I correct?
2. In COOT, when REDUCE adds hydrogens, does it move any of the non-H
atoms too to optimize geometry?
3. In COOT, does REDUCE automatically flip ASN and GLN and HIS
sidechains to optimize H-bonding?
Thank you in advance for your time in answering my questions!
Best,
‘Kate’ Sun Kyung Kim
*From: *Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
*Date: *Thursday, February 15, 2024 at 4:39 PM
*To: *Kim, Sun Kyung <kim...@llnl.gov>, COOT@JISCMAIL.AC.UK
<COOT@JISCMAIL.AC.UK>
*Subject: *Re: How does COOT determine protonation states
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>
<mailto:lucrezia.catap...@kcl.ac.uk>
*Date: *Friday, February 2, 2024 at 6:21 AM
*To: *Kim, Sun Kyung <kim...@llnl.gov> <mailto:kim...@llnl.gov>,
COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK> <mailto: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> <mailto:COOT@JISCMAIL.AC.UK> on behalf of
Kim, Sun Kyung <0000bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk>
<mailto:0000bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk>
*Date: *Tuesday, 30 January 2024 at 00:36
*To: *COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
<mailto:COOT@JISCMAIL.AC.UK>
*Subject: *How does COOT determine protonation states
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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# Generated by Coot
RESIDUE AMP 35
CONECT P 4 O1P O2P O3P O5'
CONECT O1P 1 P
CONECT O2P 1 P
CONECT O3P 1 P
CONECT O5' 2 P C5'
CONECT C5' 4 O5' C4' H5'1 H5'2
CONECT C4' 4 C5' O4' C3' H4'
CONECT O4' 2 C4' C1'
CONECT C3' 4 C4' O3' C2' H3'
CONECT C1' 4 O4' C2' N9 H1'
CONECT O3' 2 C3' HO3'
CONECT C2' 4 C3' O2' C1' H2'
CONECT O2' 2 C2' HO2'
CONECT N9 3 C1' C8 C4
CONECT C8 3 N9 N7 H8
CONECT C4 3 N9 C5 N3
CONECT N7 2 C8 C5
CONECT C5 3 N7 C6 C4
CONECT C6 3 C5 N6 N1
CONECT N6 3 C6 HN61 HN62
CONECT N1 2 C6 C2
CONECT C2 3 N1 N3 H2
CONECT N3 2 C2 C4
CONECT H5'1 1 C5'
CONECT H5'2 1 C5'
CONECT H4' 1 C4'
CONECT H3' 1 C3'
CONECT HO3' 1 O3'
CONECT H2' 1 C2'
CONECT HO2' 1 O2'
CONECT H1' 1 C1'
CONECT H8 1 C8
CONECT HN61 1 N6
CONECT HN62 1 N6
CONECT H2 1 C2
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