From 88ce19d2d06c3fdef4b367d3a44fd4ce3079e2ce Mon Sep 17 00:00:00 2001
From: Beale John Henry <beale_j@saresc-cons-04.psi.ch>
Date: Thu, 1 Feb 2024 09:08:04 +0100
Subject: [PATCH] added some instructions

---
 reduction_tools/crystfel_run.sh | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/reduction_tools/crystfel_run.sh b/reduction_tools/crystfel_run.sh
index ebf1f5c..a1e8adf 100644
--- a/reduction_tools/crystfel_run.sh
+++ b/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 \