added some instructions

reduction_tools/crystfel_run.sh

@@ -1,7 +1,13 @@
 #!/bin/bash
 
 module purge
-module load crystfel/0.10.2
+module use MX unstable
+module load crystfel/0.10.2-rhel8
+
+# add path to images
+# add output stream name
+# add path to cell
+# change threshold to 3000 if at Alvra
 
 indexamajig -i <path-to-images> \
   -o <output.steam> \
@@ -9,14 +15,14 @@ indexamajig -i <path-to-images> \
   --pdb=<path-to-cell> \
   --indexing=xgandalf-latt-cell \
   --peaks=peakfinder8 \
-  --integration=rings-nograd \
+  --integration=rings-nograd-nocen \
   --tolerance=10.0,10.0,10.0,2,3,2 \
   --threshold=10 \
   --min-snr=5 \
   --int-radius=5,5,9 \
   -j 32 \
-  --no-multi \
-  --no-retry \
+  --multi \
+  --retry \
   --check-peaks \
   --max-res=3000 \
   --min-pix-count=2 \