BioSAXS data collected at the BM29 beamline are processed and analysed by EDNA using the ATSAS package from sample-buffer subtration on.
Steps in autoprocessing are:
Reprocessing
Python scripts for re-processing can be found in /users/opd29/workspace/edna/bioSaxsv1/bin/ on slavia
Some tips for HPLC runs:
- if HPLC run didn't appear in ISPyB (appears normally only after run, not at beginning as in SC mode) check .xml of last frame for part linked to ISPyB, if missing complete lines by copy-paste from any .xml from a run which "worked" and run python /users/opd29/workspace/edna/bioSaxsv1/bin/reprocess_HPLC.py *.xml in raw folder
- if the first image empty (not a test image taken after an abort): delete its corresponding .xml and run python /users/opd29/workspace/edna/bioSaxsv1/bin/reprocess_HPLC.py *.xml in raw folder
Note: better if not other EDNA process is running, particularly in HPLC case!
Known Issues
- Occasionally DAMMIN does not finish properly. This can cause error messages from EDNA1 (=slavia) and delay in HPLC processing. Solution: log in on slavia, use top to find the PID of dammin and kill -12 PID