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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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Indicate in the backrub_seqtol protocol how long the protocol takes #20

Open momeara opened 9 years ago

momeara commented 9 years ago

For each piece of the protocol it should follow this format

1) Describe the motivation to the step and what is accomplished 2) Indicate the input files, parameters, and computational resources (e.g. running time). 3) Describe how the protocol should can be run 4) How to interpret the results

spiderbaby commented 9 years ago

The "Example command lines" section of protocols/backrub_seqtol/README.rst hopefully fulfills 1-4). I do not go into details about the generational output from seqtol as that is described in the Rosetta documentation. Links are provided in the README.

momeara commented 9 years ago 
${BENCHMARK_PATH}/protocols/backrub_seqtol/backrub_seqtol.py \
    ${BENCHMARK_PATH}/input/pdbs/2I0L_A_C_V2006/2I0L_A_C_V2006.pdb 1\
    ${BENCHMARK_PATH}/input/backrub_seqtol test_mode`

This command line took me 1 hour 45 minutes.

spiderbaby commented 9 years ago

Was that on a workstation or a laptop? That is why I am kind of against listing expected runtimes since they can vary widely depending on the hardware. The command above took me 30 minutes the other day (which is roughly what can be determined from the runtimes in the backrub and seqtol sections since backrub_seqtol.py just runs them in sequence).

On Fri, Feb 6, 2015 at 6:42 AM, momeara notifications@github.com wrote:

${BENCHMARK_PATH}/protocols/backrub_seqtol/backrub_seqtol.py ${BENCHMARK_PATH}/input/pdbs/2I0L_A_C_V2006/2I0L_A_C_V2006.pdb 1 ${BENCHMARK_PATH}/input/backrub_seqtol

This command line took me 1 hour 45 minutes.

— Reply to this email directly or view it on GitHub https://github.com/Kortemme-Lab/sequence-tolerance/issues/20#issuecomment-73246085 .

momeara commented 9 years ago

It was a workstation. If you want to say it takes at least 30 minutes that's fine, but it should give an indication that it isn't going to take 2 seconds or 2 weeks.