Next: Frequently asked questions (FAQ)
Up: Tutorial on using MODELLER
Previous: Preparing input files
Contents
Index
Running MODELLER
To run MODELLER with the script file model-default.py above, do the
following:
- 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.
- Change to the directory containing the script and alignment files using
the 'cd' command.
- Run MODELLER itself by typing the following at the command prompt:
mod8v0 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: Frequently asked questions (FAQ)
Up: Tutorial on using MODELLER
Previous: Preparing input files
Contents
Index
Ben Webb
2005-04-21