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SECPipe and SECData Documentations

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.
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: <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>]
<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.
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.