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 important<https://aka.ms/LearnAboutSenderIdentification> 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/
