Running MODELLER

To run MODELLER with the script file model-default.py above, do the following:

1. Open a command line prompt:
   • On Linux/Unix: ssh to the machine, or open an xterm or GNOME Terminal.
   • On Windows: Click on the `Modeller' link on your Start Menu. This will give you a Windows Command Prompt, set up for you to run MODELLER.
   • On Mac OS X: Open the Terminal application.

2. Change to the directory containing the script and alignment files using the 'cd' command.

3. Run MODELLER itself by typing the following at the command prompt:

   mod8v2 model-default.py

A number of intermediary files are created as the program proceeds. After about 30 seconds on a Pentium IV workstation, 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.