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Sub-directories here are:

tutorial-model\    ... sample modeling, given an alignment
align-model-steps\ ... sample alignment and modeling, given templates
all-steps\         ... sample template searching, alignment, and modeling
loop\              ... sample loop modeling, given a template
sidechain_INT\     ... sample point mutation modeling, internal development stuff
wild_card\         ... sample wild card use in an alignment file
commands\          ... sample .top files for each MODELLER command
debug-energy_INT\  ... energy testing, internal development stuff
misc_INT\          ... miscellanous, internal development stuff
atom_files\        ... atoms files for some TOP files

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To execute all .top files                    :  Run_tests.bat  1> out 2> err

To check the results                         :  Edit file 'out' and check it for any errors

To clean everything                          :  Clean_all.bat

Notes:

You need to have ASGL installed for all-steps/cluster.top not to fail
                     (FILE:  ./all-steps/./alignment.seg.log message)
