flip SA flag drop

configs/test.yaml

@@ -3,7 +3,7 @@
 # April 20, 2020
 
 project:
-  name:                 'DMPL_test'
+  name:                 'DMPL_test_final'
   rawdata_dirs:
     - '/asap3/petra3/gpfs/p11/2020/data/11009999/raw'
     - '/asap3/petra3/gpfs/p11/2020/data/11010091/raw'

scripts/dmpl.sh

@@ -92,23 +92,23 @@ cd ${outdir}
 echo "chdir: ${outdir}"
 
 
+# >> uni_free : same origin, set rfree flags to the common set
+uni_free=$SCRIPTS_DIR/uni_free.csh
+csh ${uni_free} ${input_mtz} ${metadata}_rfree.mtz ${free_mtz}
+
+
 # >> if the mtz is from staraniso, drop SA_flag
 #    http://staraniso.globalphasing.org/test_set_flags_about.html 
 #    if the mtz doesn't have the SA_flag col, this does nothing
 sftools <<eof
-READ ${input_mtz}
+READ ${metadata}_rfree.mtz
 SELECT COL SA_flag NOT absent
-WRITE ${input_mtz}
+WRITE ${metadata}_rfree.mtz
 Y
 EXIT 
 eof
 
 
-# >> uni_free : same origin, set rfree flags to the common set
-uni_free=$SCRIPTS_DIR/uni_free.csh
-csh ${uni_free} ${input_mtz} ${metadata}_rfree.mtz ${free_mtz}
-
-
 # >> cut resolution of MTZ
 cut_mtz=${metadata}_rfree_rescut.mtz
 mtzutils hklin ${metadata}_rfree.mtz \
@@ -143,10 +143,9 @@ rm fd-${cut_mtz}
 ref_pdb_list=`echo ${ref_pdb} | tr ',' ' '`
 
 
-# >> dimple round 1: MR & light refinement
-# >> dimple to check for blobs
+# >> dimple --> only purpose is to select the correct PDB to use as a ref
 dimple                                    \
-  -M0                                     \
+  -M1                                     \
   --free-r-flags ${cutdown_mtz}           \
   --jelly 0                               \
   --restr-cycles 0                        \