Hi there, I'm a bioinformatics UCT student and we've been given an assignment to solve a protein structure. Everyone has been struggling with this step and I've tried many many ways to get this to work in ChimeraX, but I get new errors every time so I'm asking for help. Sorry for the long question, but I would *highly* appreciate help at this point (and so would my class - so if I get an answer you'll be making ~30 people very happy, not just 1!) Essentially this ligand has a sulphur that makes a thioester to Cys 146, our professor said we should remove the Cys sulphur and then combine the ligand and the remainder of the ligand into one residue and name it 'AKG.' We have a dimer so we also do this in 2 places. We need to refine this using ISOLDE, which is where most of my problems appear. Then he says we can use 'AKG.xml' in residue parameterisation so ISOLDE will accept our residue. Currently the way my pdb is layed out causes chimera to only render the ligand part of AKG but not the Cys part. I don't know why, and more importantly my general understanding of how ChimeraX reads pdb files is lacking. *So I suppose finally my actual question*: what do I need to do to make it so ChimeraX renders the residue correctly, and ISOLDE accepts AKG.xml and can actually run a simulation on this pdb? I've attached: 1: AKG.xml (for residue parameterisation) 2: 5 - refine1.mtz (the electron density map data) 3: 6c - part of AKG missing.pdb (the current pdb I'm working with where the Cys part of residue 146 isn't rendered) 4: 6b - pre-covalent linking.pdb (the latest copy of the pdb I could get running in ISOLDE simulations. This has the protein dimer and 2 ligands as 3 separate models. I'd already deleted the Cys's Sulphur here so it's more like an Ala in this case) Sorry for such a massive email, but I wanted to be as specific as possible with my problem. If you could provide me some help it would be extremely helpful. Sadly our lectures for this module are over and getting our lecturer to explain anything is virtually impossible. Thanks so much, Byron (and the rest of my class to be honest)