Kortemme-Lab / sequence-tolerance

A sequence tolerance benchmark capture containing the benchmark dataset and benchmarked protocol captures.

https://kortemmelab.ucsf.edu/benchmarks

MIT License

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protocols/backrub_seqtol -> Example Overall Command Line #12

Closed momeara closed 9 years ago

momeara commented 9 years ago

Paths and Extensions

WORKING_DIRECTORY=.
BENCHMARK_PATH=<path/to/sequence-tolerance>
# edit protocols/backrub_seqtol/settings.json

Run backrub sequence tolerance in test mode

In test mode, it does restricted sampilng to test that the protocol i set up correctly

python ${SEQUENCE_TOLERANCE_BASE}/protocols/backrub_seqtol/backrub_seqtol.py ${SEQUENCE_TOLERANCE_BASE}/inputs/pdbs/2I0L_A_C_V2006/2I0L_A_C_V2006.pdb 1 test_mode

spiderbaby commented 9 years ago

I'm unsure what the bug is in this ticket - are the example command lines wrong?

momeara commented 9 years ago

It should indicate up front what paths and parameters need to be specified by the user.
The path to the input files is broken
It should say what "test mode" means

spiderbaby commented 9 years ago

Ah, I see. I updated the "Test mode" section to describe what it does in more detail, added explanations for the script parameters, and (hopefully) fixed the paths.