From 9a71a59e9929332a65632e6de170f9ae9cdf0244 Mon Sep 17 00:00:00 2001
From: Beale John Henry <beale_j@saresc-cons-04.psi.ch>
Date: Tue, 10 Oct 2023 09:25:55 +0200
Subject: [PATCH] some updates

---
 reduction_tools/crystfel_run.sh | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/reduction_tools/crystfel_run.sh b/reduction_tools/crystfel_run.sh
index c6aacca..32417b4 100644
--- a/reduction_tools/crystfel_run.sh
+++ b/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> \
-  -o <output.steam> \
-  --geometry=<path-to-geom> \
-  --pdb=<path-to-cell> \
+indexamajig -i <path-to-images> \ # change this
+  -o <output.steam> \ # change this
+  --geometry=<path-to-geom> \ # change this
+  --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 \
-  -j 36 \
+  --int-radius=3,5,9 \
+  -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