From 0bcfe3cdf917ae53764c423c7af865352af47920 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 7 Jul 2015 14:16:14 +0200
Subject: partialator: Increase maximum B factor to 1000 A^2, and normalise B
 factors

---
 src/partialator.c | 22 ++++++++++++++++++++++
 src/rejection.c   |  2 +-
 2 files changed, 23 insertions(+), 1 deletion(-)

(limited to 'src')

diff --git a/src/partialator.c b/src/partialator.c
index ef81ab43..46353c25 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -436,6 +436,27 @@ static void write_pgraph(RefList *full, Crystal **crystals, int n_crystals,
 }
 
 
+static void normalise_scales(Crystal **crystals, int n_crystals)
+{
+	int i;
+	int n = 0;
+	double sum_B = 0.0;
+	double mean_B;
+
+	for ( i=0; i<n_crystals; i++ ) {
+		if ( crystal_get_user_flag(crystals[i]) != 0 ) continue;
+		sum_B += crystal_get_Bfac(crystals[i]);
+		n++;
+	}
+	mean_B = sum_B / n;
+	STATUS("Mean B = %e A^2\n", mean_B*1e20);
+	for ( i=0; i<n_crystals; i++ ) {
+		double B = crystal_get_Bfac(crystals[i]);
+		crystal_set_Bfac(crystals[i], B-mean_B);
+	}
+}
+
+
 int main(int argc, char *argv[])
 {
 	int c;
@@ -820,6 +841,7 @@ int main(int argc, char *argv[])
 
 		show_duds(crystals, n_crystals);
 		check_rejection(crystals, n_crystals, full);
+		normalise_scales(crystals, n_crystals);
 
 		/* Re-estimate all the full intensities */
 		reflist_free(full);
diff --git a/src/rejection.c b/src/rejection.c
index a565fec3..f0d6dd3e 100644
--- a/src/rejection.c
+++ b/src/rejection.c
@@ -175,7 +175,7 @@ void check_rejection(Crystal **crystals, int n, RefList *full)
 	for ( i=0; i<n; i++ ) {
 
 		/* Reject if B factor modulus is very large */
-		if ( fabs(crystal_get_Bfac(crystals[i])) > 1e-18 ) {
+		if ( fabs(crystal_get_Bfac(crystals[i])) > 1e-17 ) {
 			crystal_set_user_flag(crystals[i], 1);
 		}
 
-- 
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