Hello,

I am attempting to attach a covalent (cysteine modifying) ligand to my protein, and I will later be optimizing/minimizing in another program.

I opened my structure in Chimera, loaded the ligands, moved them roughly into place, and merged the models. I then added the bonds and exported the file as a pdb. Upon reopening that very same pdb in Chimera, the bonds I made are gone (however, the ligands are in the position I placed them in). Curious to understand what I am doing incorrectly here.

Alex

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