Re: [COOT] How does COOT determine protonation states

2024-02-15 Thread 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&A=1



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] How does COOT determine protonation states

2024-02-15 Thread 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&A=1 
 






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







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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/