From f2d72dc8601621d3c880cb54ed0e95ed1fe2579f Mon Sep 17 00:00:00 2001
From: Beale John Henry <beale_j@saresc-vcons-01.psi.ch>
Date: Tue, 19 Sep 2023 10:39:01 +0200
Subject: [PATCH] moved to new folder

---
 reduction_tools/crystfel_run.sh | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 reduction_tools/crystfel_run.sh

diff --git a/reduction_tools/crystfel_run.sh b/reduction_tools/crystfel_run.sh
new file mode 100644
index 0000000..c6aacca
--- /dev/null
+++ b/reduction_tools/crystfel_run.sh
@@ -0,0 +1,25 @@
+/#!/bin/bash
+
+module purge
+module load crystfel/0.10.2
+
+indexamajig -i <path-to-images> \
+  -o <output.steam> \
+  --geometry=<path-to-geom> \
+  --pdb=<path-to-cell> \
+  --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 \
+  -j 36 \
+  --no-multi \
+  --no-retry \
+  --check-peaks \
+  --max-res=3000 \
+  --min-pix-count=1 \
+  --local-bg-radius=4 \
+  --min-res=85
+