SECPipe and SECData Documentations
SECPipe is an automated SEC-SAXS data real-time processing and analyis pipeline. It requires no user intervention and creates a current sample folder inside the analysis folder with the following data:
- 'sastool' folder - this is the output sastool folder containing individual scattering curves.
- 'average' folder - scattering data averaged in sets of 5
- 'plots' folder - plots showing Rg, I(0), I(qL) and UV data during the elution. The data to re-create these graphs is also saved and can also be opened with bl42-dat program.
- <sample_name_number>.bip - this file is used by Blu-Ice to display real-time Rg, I(0) and I(qL) data during the experiment.
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SECData can be run from a command line, giving a possibility to re-analyze data after the experiment.
If run without any parameters, it will output a basic how-to:
secdata.py <path to the first sample file> [path to the first buffer file, if different than sample] <first buffer number> <number of buffers> <qL pixel num> [<shut_cl_start> <shut_cl_end>]
where:
<path to the first sample file> - the path to the first image. ex)/mnt/home/b_bl42/data/BSA_0_001.tif
[path to the first buffer file, if different than sample] – the path to the first buffer image. This parameter is not required.
<first buffer number> - the 1st image number of the buffer region
<number of buffers> - the number of images to use for buffer subtraction
<qL pixel num> - default is 6, which means that the 6th lowest measured q value
<shut cl start> <shut cl end> - in case the x-ray shutter was closed for the part of the experiment, that data will not be evaluated. These parameters are not required.
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The pipeline is written in Python2 and uses analysis software from the ATSAS package by Dimitri Svergun’s group at Hamburg and our in-house image scaling and integration software SasTool. The software has been designed to be modular and easily adaptable, allowing the easy addition of new software tools as they arise.