On 2/1/20 10:58 AM, Daniel Evans wrote: > The MODELLER documentation at > https://salilab.org/modeller/manual/node149.html#MEMB:iodata.convertmodres > says the following: > > "/Some special handling is done for certain commonly-used modified > residues. The MSE residue type is mapped to the regular MET amino > acid, and the SE atom in this residue is mapped to SD. The MEX and > ABU residue types are both mapped to CYS./"
... > I recently encountered PDB ID 3OW6. This structure includes a ligand > labeled MEX. The ligand does not resemble CYS, and the presence of MEX > causes an error. I'm reluctant to set io_data.convert_modres to False, > because I'd like to handle other modified residues (ex. MSE).
This part of the Modeller code is ancient, at least 15 years old, and PDB has changed a lot since then. I don't see any examples of MEX used as a polymer in current PDB (and only 1 example of it used as a ligand, in 3ow6 as you noted) and only 3 examples of ABU polymer. Since neither MEX nor ABU look much like CYS, I will remove this code entirely from the next Modeller release - they can't be considered "commonly-used modified residues" and it is probably causing more harm than good. (Of course, if anybody relies on this ABU/MEX->CYS mapping, 1. it is easy to work around and 2. let me know!)
Ben Webb, Modeller Caretaker