This is a benchmark for IMP's SAXS Merge method and webserver.
Running the benchmark:
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
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
runapp_*folder, in which the merging of the inputs took place
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
- Run number (an index to the inputs in
- An index to a set of parameters that was used, currently this is always zero
- The name of the input folder
- The chi2 between manual and automatic merges
- The chi2 between Gaussian Process manual vs automatic mean functions
- The radius of gyration in the automatic merge, as guessed with the Guinier fit.
- Same as previously
- The radius of gyration in the manual merge, as guessed with the Guinier fit.
- Same as previously
- If a PDB is available, the radius of gyration based on the Guinier fit on the FoXS profile
- If a PDB is available, the chi2 between automatic merge and FoXS
- If a PDB is available, the chi2 between manual merge and FoXS
- If a PDB is available, the chi2 between automatic merge and crysol
- If a PDB is available, the radius of gyration based on the Guinier fit on the crysol profile
- The sigma of the Gaussian Process Interpolation on the automatic merge
- 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.
- 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