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Running MODELLER

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

  1. Open a command line prompt:

  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:

    mod8v1 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.


next up previous contents index
Next: Frequently asked questions (FAQ) Up: Tutorial on using MODELLER Previous: Preparing input files   Contents   Index
Ben Webb 2005-06-20