Some errors are recoverable. For those errors, a Python exception exception is raised. It is then up to your script to deal sensibly with the failure of the preceding command using a standard 'except' clause. For example, this flexibility allows derivation of multiple models and searching for many sequences, even if some cases abort due to convergence problems. This exception could be a generic ModellerError exception, a more specific subclass (FileFormatError), or a standard Python exception5.1.
There are five kinds of messages that MODELLER writes to the log file: long output from the MODELLER commands, short notes to do with the execution of the program (files opened, etc.), warnings identified by `_W>', errors identified by `_E>', and the messages about the status of dynamic memory allocation. To control how much of this output is displayed, use the log object; for more information, see Section 6.30.