From 4c5ade0f2491210f65be3d8283d56da60be82ff8 Mon Sep 17 00:00:00 2001
From: Beale John Henry <beale_j@saresc-cons-04.psi.ch>
Date: Thu, 1 Feb 2024 09:21:29 +0100
Subject: [PATCH] improved instructions

---
 reduction_tools/make_mtz.py | 49 +++++++++++++++++++++++++------------
 1 file changed, 34 insertions(+), 15 deletions(-)

diff --git a/reduction_tools/make_mtz.py b/reduction_tools/make_mtz.py
index 8d74892..ca3c443 100644
--- a/reduction_tools/make_mtz.py
+++ b/reduction_tools/make_mtz.py
@@ -6,8 +6,27 @@
 # aim
 to make an mtz from an hkl file output from partialator or process_hkl
 
-# usage
-python make_mtz.py 
+# usage to make mtz from manually entered lengths and angles
+python make_mtz.py -i <path to .hkl file from partialator>
+                   -o name of .mtz file
+                   -p project name in mtz
+                   -x xtal name in mtz
+                   -d dataset name in mtz
+                   -g spacegroup
+                   -c list of cell lengths and angles to use - 59.3,59.3,153.1,90.0,90.0,90.0
+
+# usage to make mtz from the mean angles and lengths in stream file
+python make_mtz.py -i <path to .hkl file from partialator>
+                   -o name of .mtz file
+                   -p project name in mtz
+                   -x xtal name in mtz
+                   -d dataset name in mtz
+                   -g spacegroup
+                   -s <path to stream file>
+                   -u True
+
+# usage to get list of mean lengths and angles from stream files
+python make_mtz.py -s <path to stream file>
 
 # output
 - .mtz file
@@ -128,19 +147,7 @@ if __name__ == "__main__":
         "-o",
         "--mtzout",
         help="name of mtz out file. The default will by the hklin with .mtz appended",
-        type=str,
-    )
-    parser.add_argument(
-        "-c",
-        "--cell",
-        help="list of complete cell length and angles, e.g. 59.3,59.3,153.1,90.0,90.0,90.0. They all should be floats",
-        type=list_of_floats
-    )
-    parser.add_argument(
-        "-s",
-        "--stream_file",
-        help="this will simply output the mean unit cell for the subsequent make_mtz run",
-        type=os.path.abspath,
+        type=str
     )
     parser.add_argument(
         "-p",
@@ -169,6 +176,18 @@ if __name__ == "__main__":
         help="spacegroup for making mtz, e.g P41212",
         type=str
     )
+    parser.add_argument(
+        "-c",
+        "--cell",
+        help="list of complete cell length and angles, e.g. 59.3,59.3,153.1,90.0,90.0,90.0. They all should be floats",
+        type=list_of_floats
+    )
+    parser.add_argument(
+        "-s",
+        "--stream_file",
+        help="this will simply output the mean unit cell for the subsequent make_mtz run",
+        type=os.path.abspath,
+    )
     parser.add_argument(
         "-u",
         "--use_stream",