Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

On 22/02/2024 01:06, Kim, Sun Kyung wrote:


Hi Paul,

Thank you for your response!

I opened Coot from my terminal, and not seeing any diagnostic 
information, but it just opens up coot.


There seems to be some confusion because I read this and think "that 
cannot be." Are you reading what is going on in the terminal? It should 
be something like this:



phemius src% coot
INFO:: built with GTK 4.12.4
pdd /usr/local/Cellar/coot/1.1.06/share/coot
There are 143 data in 
/usr/local/Cellar/coot/1.1.06/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in 
/usr/local/Cellar/coot/1.1.06/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in 
/usr/local/Cellar/coot/1.1.06/share/coot/lib/data/monomers/a/ASP.cif

...


When you mention I could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers… 
I’m not sure as to what those files are or where I can find them.. are 
there documentations to this that I can refer to?


One can use the copy of the CCP4 Monomer library that comes with the 
CCP4 Suite.


Or one can download it from github:

https://github.com/MonomerLibrary/monomers/archive/refs/tags/ccp4-8.0.016.tar.gz

rename or link monomers-ccp4-8.0.016 to monomers

put the monomers in a directory called data

Then set the environment varable COOT_REFMAC_LIB_DIR to the directory 
that contains data.


It’s strange that COOT starts having this issue for me all of a 
sudden. The only thing I can think of is, over the weekend I had to do 
some mandatory upgrades to my government computer that I’m using…do 
you think any updates to the MacOS or something like that could have 
caused this issue for me?



Typically one used to need to reinstall XQuartz after doing an OS update.

But I suspect something more fundamental/trivial in your setup.


Thank you for your help as always!



You're welcome


Paul.



Best,

‘Kate’ Sun Kyung Kim

*From: *Paul Emsley 
*Date: *Wednesday, February 21, 2024 at 9:35 AM
*To: *Kim, Sun Kyung , COOT@JISCMAIL.AC.UK 


*Subject: *Re: How does COOT determine protonation states

On 21/02/2024 02:50, Kim, Sun Kyung wrote:

Thank you Paul for that information. I will look into Acedrg and
Grade2!

Sounds good.

I have an unrelated question… I’ve never encountered this before,
but all of a sudden my COOT is complaining that it doesn’t have
restraints for refinement… (screenshot attached)… any idea why
this error message is suddenly appearing?

Coot writes diagnostic information to the terminal/console/program 
from where it was started. You need to get access to that information.


I would try to start Coot from a terminal and see what it says about 
dictionaries and libraries as it starts up.


Before invoking coot, you could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers - 
how to do that depends on your system.


Regards,

Paul.





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Re: [COOT] How does COOT determine protonation states

[Kim, Sun Kyung]

Hi Paul,

Thank you for your response!

I opened Coot from my terminal, and not seeing any diagnostic information, but 
it just opens up coot.

When you mention I could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers… I’m not 
sure as to what those files are or where I can find them.. are there 
documentations to this that I can refer to? Thank you.

It’s strange that COOT starts having this issue for me all of a sudden. The 
only thing I can think of is, over the weekend I had to do some mandatory 
upgrades to my government computer that I’m using…do you think any updates to 
the MacOS or something like that could have caused this issue for me?

Thank you for your help as always!


Best,
‘Kate’ Sun Kyung Kim

From: Paul Emsley 
Date: Wednesday, February 21, 2024 at 9:35 AM
To: Kim, Sun Kyung , COOT@JISCMAIL.AC.UK 
Subject: Re: How does COOT determine protonation states


On 21/02/2024 02:50, Kim, Sun Kyung wrote:

Thank you Paul for that information. I will look into Acedrg and Grade2!



Sounds good.

I have an unrelated question… I’ve never encountered this before, but all of a 
sudden my COOT is complaining that it doesn’t have restraints for refinement… 
(screenshot attached)… any idea why this error message is suddenly appearing?


Coot writes diagnostic information to the terminal/console/program from where 
it was started. You need to get access to that information.

I would try to start Coot from a terminal and see what it says about 
dictionaries and libraries as it starts up.

Before invoking coot, you could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers - how to 
do that depends on your system.

Regards,

Paul.





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Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

On 21/02/2024 02:50, Kim, Sun Kyung wrote:


Thank you Paul for that information. I will look into Acedrg and Grade2!



Sounds good.

I have an unrelated question… I’ve never encountered this before, but 
all of a sudden my COOT is complaining that it doesn’t have restraints 
for refinement… (screenshot attached)… any idea why this error message 
is suddenly appearing?



Coot writes diagnostic information to the terminal/console/program from 
where it was started. You need to get access to that information.


I would try to start Coot from a terminal and see what it says about 
dictionaries and libraries as it starts up.


Before invoking coot, you could try setting COOT_MONOMER_LIB_DIR or 
REFMAC_MONOMER_LIB_DIR to the directory that containers the monomers - 
how to do that depends on your system.


Regards,

Paul.



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Re: [COOT] How does COOT determine protonation states

[Kim, Sun Kyung]

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 
Date: Thursday, February 15, 2024 at 4:39 PM
To: Kim, Sun Kyung , 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 

Date: Friday, February 2, 2024 at 6:21 AM
To: Kim, Sun Kyung , 
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 
 on behalf of Kim, Sun Kyung 

Date: Tuesday, 30 January 2024 at 00:36
To: COOT@JISCMAIL.AC.UK 

Subject: How does COOT determine protonation states
Some people who received this message don't often get email from 
bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk.
 Learn why this is 
important
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



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1



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Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

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 
*Date: *Thursday, February 15, 2024 at 4:39 PM
*To: *Kim, Sun Kyung , 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 

*Date: *Friday, February 2, 2024 at 6:21 AM
*To: *Kim, Sun Kyung  ,
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
  on behalf of
Kim, Sun Kyung 

*Date: *Tuesday, 30 January 2024 at 00:36
*To: *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

Re: [COOT] How does COOT determine protonation states

[Paul Emsley]

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 
*Date: *Friday, February 2, 2024 at 6:21 AM
*To: *Kim, Sun Kyung , 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 
 on behalf of Kim, Sun Kyung 


*Date: *Tuesday, 30 January 2024 at 00:36
*To: *COOT@JISCMAIL.AC.UK 
*Subject: *How does COOT determine protonation states




Some people who received this message don't often get email from 
bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk. Learn why this is 
important 





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



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 
 






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Re: [COOT] How does COOT determine protonation states

[Kim, Sun Kyung]

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 
Date: Friday, February 2, 2024 at 6:21 AM
To: Kim, Sun Kyung , 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 
 on behalf of Kim, Sun Kyung 

Date: Tuesday, 30 January 2024 at 00:36
To: COOT@JISCMAIL.AC.UK 
Subject: How does COOT determine protonation states
Some people who received this message don't often get email from 
bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk. Learn why this is 
important
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



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1



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Re: [COOT] How does COOT determine protonation states

[Bernhard Lohkamp]

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
>  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 ade43f7741e4-dmarc-
> requ...@jiscmail.ac.uk. Learn why this is important
> 
>
>
> 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
>  on behalf of Kim, Sun Kyung  dmarc-requ...@jiscmail.ac.uk>
> Date: Tuesday, 30 January 2024 at 00:36
> To: COOT@JISCMAIL.AC.UK 
> Subject: How does COOT determine protonation states
>
>   Some people who received this message don't often get email from
> bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk. Learn why this is
> important 
>
>
>
> 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
>
>
>
> 
>
> To unsubscribe from the COOT list, click the following link:
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This 

Re: [COOT] How does COOT determine protonation states

[Lucrezia Catapano]

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 
 on behalf of Kim, Sun Kyung 

Date: Tuesday, 30 January 2024 at 00:36
To: 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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Re: [COOT] How does COOT determine protonation states

[Bernhard Lohkamp]

> 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?

Coot uses (in this case) the programme/method reduce from the Richardson lab to 
add hydrogens. You will find more information on reduce here:

http://kinemage.biochem.duke.edu/software/reduce/

HTH,

B

>
> Thank you for your time answering this question, much appreciated!
>
>
>
> Best,
>
> ‘Kate’ Sun Kyung Kim
>
>
> 
>
> To unsubscribe from the COOT list, click the following link:
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***

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


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[COOT] How does COOT determine protonation states

[Kim, Sun Kyung]

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



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
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