SAXS Merge benchmark

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

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:

• a runapp_* folder, in which the merging of the inputs took place
• a compapp_* folder, in which manual and automatic merges are compared

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

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:

Testable: Yes.

Parallelizeable: Yes

Publications:

• Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M, J Synchrotron Radiat, (2014) 21, 203-8
• Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A, Nucleic Acids Res, (2014) 42, D336-46
• see also warning notice on the SAXS Merge website