I have noticed that some HETATM records are read by Modeller and automatically handled as corresponding standard residues (for example MSE -> MET), even if env.io.hetatm is set to False. It is explained at http://salilab.org/modeller/9.9/manual/node171.html.
I would like to know if you could suggest a way to disable this behaviour and really ignore all HETATM records.
I have tried to remove the MSE line from restyp.lib and provide my reduced restyp.lib with env = environ(restyp_lib_file='myrestyp.lib'), but this does not seem to work as the MSE still appears to be read and taken into account as MET by Modeller.
Thanks for your time,