Create subvolume fixed and cleaned

kernel/2dx_merge/scripts-merge3D/2dx_generateMergeMap.script

@@ -228,7 +228,7 @@ source ${proc_2dx}/2dx_extend_map.com volume.map extended.map
 echo "# IMAGE: extended.map <MAP: final map 3D, 2x2 unit cells>"  >> LOGS/${scriptname}.results
 #
 if ( ${calculate_subvolume}x != "0x" ) then 
-    source ${proc_2dx}/2dx_create_subvolume.com extended.map ${realcell} ${ALAT} 3D_sub.map
+    source ${proc_2dx}/2dx_create_subvolume.com ${calculate_subvolume} extended.map ${realcell} ${ALAT} 3D_sub.map
     #
     echo "# IMAGE-IMPORTANT: 3D_sub.map <MAP: 3D sub map>" >> LOGS/${scriptname}.results
     #

kernel/2dx_merge/scripts-merge3D/2dx_sharpenRefinedMap.script

@@ -112,7 +112,7 @@ if(${sharpening_algo} == "1") then
     \rm -f ${bead_model_sub_map}
     #
     if ( ${calculate_subvolume}x != "0x" ) then 
-        source ${proc_2dx}/2dx_create_subvolume.com ${bead_model_extended_map} ${realcell} ${ALAT} ${bead_model_sub_map}
+        source ${proc_2dx}/2dx_create_subvolume.com ${calculate_subvolume} ${bead_model_extended_map} ${realcell} ${ALAT} ${bead_model_sub_map}
         #
         echo "# IMAGE-IMPORTANT: ${bead_model_sub_map} <Bead model sub map>" >> LOGS/${scriptname}.results
     endif
@@ -226,7 +226,7 @@ if(${sharpening_algo} != "0" || ${if_bfactor_sharpen} == "y") then
     \rm -f ${sharpened_sub_map}
     #
     if ( ${calculate_subvolume}x != "0x" ) then 
-        source ${proc_2dx}/2dx_create_subvolume.com ${sharpened_extended_map} ${realcell} ${ALAT} ${sharpened_sub_map}
+        source ${proc_2dx}/2dx_create_subvolume.com ${calculate_subvolume} ${sharpened_extended_map} ${realcell} ${ALAT} ${sharpened_sub_map}
         #
         echo "# IMAGE-IMPORTANT: ${sharpened_sub_map} <Sharpened sub map>" >> LOGS/${scriptname}.results
     endif

kernel/config/2dx_master.cfg

@@ -3789,12 +3789,12 @@ set npo_line2 = "MODE BELOW 0 DASHED 1 0.15 0"
 # LABEL: Calculate Sub-Volume also?
 # LEGEND: Switch, deciding if a smaller sub-volume should also be calculated. The details of the selection of the sub-volume have to be adjusted directly within the calling script. There are a few possible sub-scripts available. Choose one, or adjust one to your special needs.
 # EXAMPLE: calculate_subvolume = "n"
-# TYPE: Drop_Down_Menu "0=No;1=Yes, Sub-Volume Type 1 (MloK1);2==Yes, Sub-Volume Type 2 (CitS);3=Yes, Sub-Volume Type 3 (Alex);4=Yes, Sub-Volume Type 4 (Aqp);5=Yes, Sub-Volume Type 5 (ClC);6=Yes, Sub-Volume Type 6 (FhuA);7=Yes, Sub-Volume Type 7"
+# TYPE: Drop_Down_Menu "0=No;1=Sub-Volume Type 1 (MloK1);2=Sub-Volume Type 2 (CitS);3=Sub-Volume Type 3 (Aqp);4=Sub-Volume Type 4(ClC);5=Sub-Volume Type 5 (FhuA)"
 # HELP: http://2dx.org/documentation/2dx-software/parameters/Subvolume
 # INHERITABLE_UPON_INIT: NO
 # SYNC_WITH_UPPER_LEVEL: NO
 # USERLEVEL: SIMPLE
-set calculate_subvolume = "4"
+set calculate_subvolume = "0"
 #
 # LABEL: Mask Sub-Volume with PDB file (Does not yet work)?
 # LEGEND: Switch, deciding if the obtained sub-volue should be masked so that only the densities within a certain radius of a specified PDB file should be kept.

kernel/proc/2dx_create_subvolume.com

@@ -2,19 +2,20 @@
 # 2dx_create_subvolume.com
 # A script to create a subvolume from a ccp4 map (extended map)
 # Usage:
-#	2dx_create_subvolume.com <input_extended_map> <real_cell> <ALAT> <output_map>
+#	2dx_create_subvolume.com <subvolume_type> <input_extended_map> <real_cell> <ALAT> <output_map>
 #
 # Example Usage:
-#	2dx_create_subvolume.com input_extended.map 131,131 200 input_sub.map
+#	2dx_create_subvolume.com 1 input_extended.map 131,131 200 input_sub.map
 #
-########################################################################
+#-----------------------------------------------------------------------
 # Prepare input and parameters
-########################################################################
+#-----------------------------------------------------------------------
 #
-set input_map = "${1}"
-set realcell = "${2}"
-set ALAT = "${3}"
-set output_map = "${4}"
+set calculate_subvolume = "${1}"
+set input_map = "${2}"
+set realcell = "${3}"
+set ALAT = "${4}"
+set output_map = "${5}"
 #
 set split = ($realcell:as/,/ /)
 set cellx = $split[1]
@@ -27,83 +28,170 @@ set ALATm1 = `echo ${ALAT} | awk '{ s = $1 - 1 } END {print s}'`
 #
 set input_name = "`echo ${input_map} | cut -d'.' -f1`"
 #
-if ( ${calculate_subvolume}x != "0x" ) then  
+#
+#
+#############################################################################
+# Set the Rotational and Translational properties for various subvolume types
+#############################################################################
+#
+#
+#
+if ( ${calculate_subvolume}x == "1x" ) then
   #------------------------------------------------------------------------
-  ${proc_2dx}/linblock "Creating subvolume of ccp4 map ${input_map}."
+  ${proc_2dx}/linblock "Creating subvolume with type MLOK1 for map ${input_map}."
   #------------------------------------------------------------------------
-  set full_cell_map = "${input_name}_full_cell.map"
+  set maprot_rota = "0.0 0.0 45.0"
+  set maprot_trans = "0.0 -20.0 0.0"
   #
-  \rm -f ${full_cell_map}
+  set middlex = "0.45"
+  set middley = "0.45"
+  set diam = "0.82"
   #
+  set limxmin = `echo ${middlex} ${diam} | awk '{ s = $1 - ( $2 / 2.0 ) } END { print s }'`
+  set limxmax = `echo ${middlex} ${diam} | awk '{ s = $1 + ( $2 / 2.0 ) } END { print s }'`
+  set limymin = `echo ${middley} ${diam} | awk '{ s = $1 - ( $2 / 2.0 ) } END { print s }'`
+  set limymax = `echo ${middley} ${diam} | awk '{ s = $1 + ( $2 / 2.0 ) } END { print s }'`
+  set limzmin = "0.0"
+  set limzmax = "1.0"
+  #
+endif
+#
+#
+#
+if ( ${calculate_subvolume}x == "2x" ) then
   #------------------------------------------------------------------------
-  ${proc_2dx}/linblock "MAPMASK - to produce map which covers full unit cell"
+  ${proc_2dx}/linblock "Creating subvolume with type CITS for map ${input_map}."
   #------------------------------------------------------------------------
-  ${bin_ccp4}/mapmask mapin ${input_map} mapout ${full_cell_map} << eof
-XYZLIM CELL
-END
-eof
+  set maprot_rota = "0.0 0.0 22.5"
+  set maprot_trans = "18.0 0.0 0.0"
+  set limxmin = "0.03"
+  set limxmax = "0.97"
+  set limymin = "0.1"
+  set limymax = "0.625"
+  set limzmin = "0.0"
+  set limzmax = "1.0"
   #
+endif
+#
+#
+#
+if ( ${calculate_subvolume}x == "3x" ) then
   #------------------------------------------------------------------------
-  ${proc_2dx}/linblock "MAPROT - to rotate volume for sub-volume preparation"
+  ${proc_2dx}/linblock "Creating subvolume with type AQP for map ${input_map}."
   #------------------------------------------------------------------------
+  set maprot_rota = "0.0 0.0 45.0"
+  set maprot_trans = "0.0 0.0 0.0"
+  set limxmin = "0.4"
+  set limxmax = "0.99"
+  set limymin = "0.4"
+  set limymax = "0.99"
+  set limzmin = "0.0"
+  set limzmax = "1.0"
   #
-  set rot_map = "${input_name}_rotated.map"
-  #
-  echo ${rot_map}
-  #
-  \rm -f ${rot_map}
+endif
+#
+#
+#
+if ( ${calculate_subvolume}x == "4x" ) then
+  #------------------------------------------------------------------------
+  ${proc_2dx}/linblock "Creating subvolume with type CLC for map ${input_map}."
+  #------------------------------------------------------------------------
+  set maprot_rota = "0.0 0.0 52.5"
+  set maprot_trans = "70.0 -10.0 0.0"
+  set limxmin = "0.17"
+  set limxmax = "0.71"
+  set limymin = "0.05"
+  set limymax = "0.92"
+  set limzmin = "0.0"
+  set limzmax = "1.0"
   #
-  set ALAT2 = `echo ${ALAT} | awk '{ s = $1 / 2.0 } END { print s }'`
+endif
+#
+#
+#
+if ( ${calculate_subvolume}x == "5x" ) then
+  #------------------------------------------------------------------------
+  ${proc_2dx}/linblock "Creating subvolume with type FHUA for map ${input_map}."
+  #------------------------------------------------------------------------
+  set maprot_rota = "0.0 0.0 0.0"
+  set maprot_trans = "0.0 0.0 0.0"
+  set limxmin = "-0.25"
+  set limxmax = "1.0"
+  set limymin = "-1.0"
+  set limymax = "0.25"
+  set limzmin = "-0.25"
+  set limzmax = "0.07"
   #
-  ${bin_ccp4}/maprot mapin ${full_cell_map} wrkout ${rot_map} << eot
+endif
+#
+#
+#
+#
+echo ":Rotating with: ${maprot_rota}"
+echo ":Translating with: ${maprot_trans}"
+echo ":Limits are: ${limxmin} to ${limxmax}, ${limymin} to ${limymax}, ${limzmin} to ${limzmax}"
+#
+#
+#
+#
+############################################################################
+# PREPARING VOLUMES
+############################################################################
+set full_cell_map = "${input_name}_full_cell.map"
+#
+\rm -f ${full_cell_map}
+#
+#------------------------------------------------------------------------
+${proc_2dx}/linblock "MAPMASK - to produce map which covers full unit cell"
+#------------------------------------------------------------------------
+${bin_ccp4}/mapmask mapin ${input_map} mapout ${full_cell_map} << eof
+XYZLIM CELL
+END
+eof
+#
+#------------------------------------------------------------------------
+${proc_2dx}/linblock "MAPROT - to rotate volume for sub-volume preparation"
+#------------------------------------------------------------------------
+#
+set rot_map = "${input_name}_rotated.map"
+#
+echo ${rot_map}
+#
+\rm -f ${rot_map}
+#
+set ALAT2 = `echo ${ALAT} | awk '{ s = $1 / 2.0 } END { print s }'`
+#
+${bin_ccp4}/maprot mapin ${full_cell_map} wrkout ${rot_map} << eot
 MODE FROM
 CELL WORK ${realcell} ${ALAT} 90.0 90.0 ${realang}
 GRID WORK ${cellx} ${celly} ${ALAT}
 XYZLIM 0 ${cellxm1} 0 ${cellym1} 0 ${ALATm1}
 SYMM WORK 1
 AVER
-ROTA POLAR 0.0 0.0 45.0
-TRANS  0.0 -20.0 0.0
+ROTA POLAR ${maprot_rota}
+TRANS  ${maprot_trans}
 eot
-  #
-  #
-  #------------------------------------------------------------------------
-  ${proc_2dx}/linblock "MAPAMSK - to cut sub-volume"
-  #------------------------------------------------------------------------
-  #   
-  # 0.7071 = 1/sqrt(2)
-  set middlex = "0.45"
-  set middley = "0.45"
-  set diam = "0.82"
-  #
-  set limxmin = `echo ${middlex} ${diam} | awk '{ s = $1 - ( $2 / 2.0 ) } END { print s }'`
-  set limxmax = `echo ${middlex} ${diam} | awk '{ s = $1 + ( $2 / 2.0 ) } END { print s }'`
-  set limymin = `echo ${middley} ${diam} | awk '{ s = $1 - ( $2 / 2.0 ) } END { print s }'`
-  set limymax = `echo ${middley} ${diam} | awk '{ s = $1 + ( $2 / 2.0 ) } END { print s }'`
-  #
-  echo ":Limits are ${limxmin} to ${limxmax}, ${limymin} to ${limymax}"
-  #
-  set processed_sub_map = "${input_name}_sub.map"
-  #
-  \rm -f ${processed_sub_map}
-  #
-  #
-  ${bin_ccp4}/mapmask mapin ${rot_map} mapout ${processed_sub_map} << eof
+#
+#
+#------------------------------------------------------------------------
+${proc_2dx}/linblock "MAPAMSK - to cut sub-volume"
+#------------------------------------------------------------------------
+#
+set processed_sub_map = "${input_name}_sub.map"
+#
+\rm -f ${processed_sub_map}
+#
+${bin_ccp4}/mapmask mapin ${rot_map} mapout ${processed_sub_map} << eof
 AXIS X,Y,Z
 scale factor 1
-xyzlim ${limxmin} ${limxmax} ${limymin} ${limymax} 0.0 1.0
+xyzlim ${limxmin} ${limxmax} ${limymin} ${limymax} ${limzmin} ${limzmax}
 pad -100
 SYMM 1
 END
 eof
-  #
-  #
-  #
-  \rm -f ${full_cell_map}
-  \rm -f ${rot_map}
-  \mv -f ${processed_sub_map} ${output_map}
-  #
-endif
-
-#############################################################################
-
+#
+#
+\rm -f ${full_cell_map}
+\rm -f ${rot_map}
+\mv -f ${processed_sub_map} ${output_map}
+#

kernel/proc/2dx_refineMergedMap_sub.com

@@ -43,7 +43,7 @@ echo "# IMAGE-IMPORTANT: ${back_projected_extended_map} <Back-Projected extended
 \rm -f ${back_projected_sub_map}
 #
 if ( ${calculate_subvolume}x != "0x" ) then 
-    source ${proc_2dx}/2dx_create_subvolume.com ${back_projected_extended_map} ${realcell} ${ALAT} ${back_projected_sub_map}
+    source ${proc_2dx}/2dx_create_subvolume.com ${calculate_subvolume} ${back_projected_extended_map} ${realcell} ${ALAT} ${back_projected_sub_map}
     #
     echo "# IMAGE-IMPORTANT: ${back_projected_sub_map} <Back-Projected sub map>" >> LOGS/${scriptname}.results
     #