Hi Omar, If there is a homologous structure with the PLP bound, I would try to do it by taking both the lysine and the PLP from that structure, instead of just the PLP. After superimposing I would save the (superimposed) coordinates and then just use a text-editor on the PDB file to replace both the lysine and PLP atoms to make your composite model. Or, depending on how the superposition looks, maybe part of the lysine. You would need to look and see which set of atoms to replace depending on where they diverge in your model, in other words, where you think you can make a semi-reasonable bond between the homologous structure atoms and your af3 model atoms. Or, you can measure all the torsion angles in the homologous lysine and then change each torsion angle in the corresponding lysine of your current model to be the same. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#adjust> Whether you try the above or not: For local minimization, one possibility is to try using Chimera instead of ChimeraX. Chimera has a general Minimize Structure tool that can handle many nonstandard residues, not yet available in ChimeraX: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize...> Although ChimeraX currently has some limited minimization capabilities, they are only for standard residues and would not include PLP. If you get an extra bundle "TugLigands" from the ChimeraX Toolshed, it might include PLP. However, I don't know if it includes PLP, and even if it does, I don't know if using this would work for a covalently bound ligand. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxtugligands> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Nov 20, 2024, at 2:54 AM, Omar De Bei via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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