To run MODELLER with the script file model-default.py above, do the following:
A number of intermediary files are created as the program proceeds. After about 10 seconds on a modern PC, the final 1fdx model is written to file 1fdx.B99990001.pdb. Examine the model-default.log file for information about the run. In particular, one should always check the output of the alignment.check() command, which you can find by searching for `check_a'. Also, check for warning and error messages by searching for `W>' and `E>', respectively. There should be no error messages; most often, there are some warning messages that can usually be ignored.
(Note: if you have Python installed on your system, you may be able to use MODELLER as an ordinary Python module. This works automatically on Mac OS X, Windows with Python 2.3 or 2.4, or using the RPM install on Linux with Python 2.3 or 2.4. On other systems, you may need to set the PYTHONPATH and LD_LIBRARY_PATH variables, or create symlinks to the relevant directories, so that your system can find the MODELLER Python modules and dynamic libraries, respectively.)