Save a residue as mmCIF template

[Tristan Croll]

Would be great to have the ability to save a given residue as a mmCIF template for future use, since some of the official templates on the CCD really aren't all that good. Many have weird/non-physiological protonation states, and for others the "ideal" geometry is not particularly ideal. I'll attach a copy of phosphatidylcholine (PC1) as an example - perhaps you might see this conformation in a vacuum, but it's like nothing you'll ever see in any physiological environment. The experimental coordinates for many of these aren't much help, since they're often missing atoms. For at least a subset of the most commonly used ligands, I'd like to be able to fix the protonation and/or energy-minimise into a real-world map and then save as a template to bundle in with ISOLDE.

[Tristan Croll]

"Ideal" coordinates in the template for PC1

[Greg Couch]

So, other than the coordinates, all of the other information in CCD entry would be the same? So, for example, no chirality change? Another option would be to limit the output to the subset that ChimeraX's mmCIF reader uses. And another option would be to target what the PDBe choose for the chem_comp and chem_comp_bond tables in their updated mmCIF files.

[Tristan Croll]

Yes, I'd be fine with that: just take the CIF file from the CCD and 
update its coordinates.

On 2020-04-16 06:56, ChimeraX wrote:

[Tristan Croll]

An add-on to this: it would also be really great to be able to create a TmplResidue from an existing Residue. The isolde add ligand command currently supports adding any residue in the components dictionary, but I'd like to extend that to allow them to add their own custom residues.