Dear ChimeraX Community,

I’m reaching out for advice on what is likely a simple issue, but I’m stuck and would greatly appreciate your input.

I’m currently working on a PLP-dependent enzyme and have generated its structure using AlphaFold3. Unfortunately, AlphaFold3 does not include PLP as a preset ligand. To address this, I’m attempting to manually add the PLP to the predicted structure based on homology with other PLP-dependent enzymes.

Here’s where I’m facing trouble:
The PLP forms a covalent bond with a lysine residue in the active site. After aligning my AlphaFold-predicted structure with the PDB structure of a homologous enzyme, I managed to position the PLP within the predicted structure. However, the lysine residue is not in the correct orientation to form the covalent bond.

I’ve tried changing the lysine’s rotamer to improve the position, but it’s still not quite right. I was considering performing a local minimization of the structure to refine the geometry, but I’m unsure how to do this in ChimeraX.

Does ChimeraX offer a tool or feature for local minimization that could help in this scenario? If so, could you guide me on how to proceed?

Thank you in advance for your help!

Best regards,

Omar