Re: [modeller_usage] Molecules MEX and CME

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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