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Thank you Paul for that information. I will look into Acedrg and Grade2! 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? [cid:image001.png@01DA642D.BD5E22E0] Thank you. Best, ‘Kate’ Sun Kyung Kim From: Paul Emsley <[log in to unmask]> Date: Tuesday, February 20, 2024 at 3:15 PM To: Kim, Sun Kyung <[log in to unmask]>, [log in to unmask] <[log in to unmask]> Subject: Re: How does COOT determine protonation states 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 <[log in to unmask]><mailto:[log in to unmask]> Date: Thursday, February 15, 2024 at 4:39 PM To: Kim, Sun Kyung <[log in to unmask]><mailto:[log in to unmask]>, [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]><mailto:[log in to unmask]> 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 <[log in to unmask]><mailto:[log in to unmask]> Date: Friday, February 2, 2024 at 6:21 AM To: Kim, Sun Kyung <[log in to unmask]><mailto:[log in to unmask]>, [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]><mailto:[log in to unmask]> 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 <[log in to unmask]><mailto:[log in to unmask]> on behalf of Kim, Sun Kyung <[log in to unmask]><mailto:[log in to unmask]> Date: Tuesday, 30 January 2024 at 00:36 To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]><mailto:[log in to unmask]> 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! 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