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SAXS Merge benchmark

Benchmark of the SAXS Merge method PubMed logo

tickVerified to work with the latest stable IMP release (2.9.0). The files are also available at GitHub.
Additional software needed to use these files: IMP numpy scipy install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp numpy scipy

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp python/numpy python/scipy
Tags benchmark SAXS

DOI

This is a benchmark for IMP's SAXS Merge method and webserver.

Running the benchmark:

Just run test/test_benchmark.py. You need gnuplot if you want to make plots. The benchmark will run saxs merge on all test systems in the input/ folder. All inputs contain an experimental SAXS profile. Some of them contain a PDB structure, whose SAXS profile is computed using FoXS and crysol. Comparisons are then also made using these profiles.

The benchmark takes about 1h to run. Check example_output for an example of the output of the benchmark. It will produce two types of folders per run:

In addition, a file bench_*.dat is produced, which contains statistics on the merge. Its columns are

  1. Run number (an index to the inputs in input/)
  2. An index to a set of parameters that was used, currently this is always zero
  3. The name of the input folder
  4. The chi2 between manual and automatic merges
  5. The chi2 between Gaussian Process manual vs automatic mean functions
  6. The radius of gyration in the automatic merge, as guessed with the Guinier fit.
  7. Same as previously
  8. The radius of gyration in the manual merge, as guessed with the Guinier fit.
  9. Same as previously
  10. If a PDB is available, the radius of gyration based on the Guinier fit on the FoXS profile
  11. If a PDB is available, the chi2 between automatic merge and FoXS
  12. If a PDB is available, the chi2 between manual merge and FoXS
  13. If a PDB is available, the chi2 between automatic merge and crysol
  14. If a PDB is available, the radius of gyration based on the Guinier fit on the crysol profile
  15. The sigma of the Gaussian Process Interpolation on the automatic merge
  16. The sigma of the Gaussian Process Interpolation on the manual merge

Finally, a large number of png files describe visually the inputs and the outputs. Their name is self-explanatory.

Notice that this benchmark was originally part of an article, which we decided not to publish. See the warning notice on the SAXS Merge website

Information

Author(s): Yannick G. Spill

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version: build info build info

Testable: Yes.

Parallelizeable: Yes

Publications: