some updates

reduction_tools/crystfel_run.sh

@@ -1,25 +1,25 @@
-/#!/bin/bash
+#!/bin/bash
 
 module purge
 module load crystfel/0.10.2
 
-indexamajig -i <path-to-images> \
+indexamajig -i <path-to-images> \ # change this
-  -o <output.steam> \
+  -o <output.steam> \ # change this
-  --geometry=<path-to-geom> \
+  --geometry=<path-to-geom> \ # change this
-  --pdb=<path-to-cell> \
+  --pdb=<path-to-cell> \ # change this
   --indexing=xgandalf-latt-cell \
   --peaks=peakfinder8 \
   --integration=rings-grad \
   --tolerance=10.0,10.0,10.0,2,3,2 \
   --threshold=10 \
   --min-snr=5 \
-  --int-radius=3,5,1 \
+  --int-radius=3,5,9 \
-  -j 36 \
+  -j 32 \
   --no-multi \
   --no-retry \
   --check-peaks \
   --max-res=3000 \
-  --min-pix-count=1 \
+  --min-pix-count=2 \
   --local-bg-radius=4 \
   --min-res=85