Generate Image Maps script moved to end of merging scripts

kernel/2dx_merge/scripts-custom/2dx_mergeCustom.script

@@ -43,6 +43,7 @@
 # DISPLAY: MergeNCYCLS
 # DISPLAY: MergeMPRINT
 # DISPLAY: MergeAK
+# DISPLAY: AMP_Scale_Factor
 # DISPLAY: MergeIWF
 # DISPLAY: MergeIWP
 # DISPLAY: max_amp_correction
@@ -84,6 +85,7 @@ set MergeBINSIZ = ""
 set MergeNCYCLS = ""
 set MergeMPRINT = ""
 set MergeAK = ""
+set AMP_Scale_Factor = ""
 set MergeIWF = ""
 set MergeIWP = ""
 set max_amp_correction = ""
@@ -131,6 +133,12 @@ if ( `echo ${RESMIN} ${RESMAX} | awk '{ if ( $1 < $2 ) { s = 1 } else { s = 0 }}
   echo "set RESMAX = ${RESMAX}" >> LOGS/${scriptname}.results
 endif
 #
+if ( ${AMP_Scale_Factor}x == ‘x’ ) then
+  set AMP_Scale_Factor = 0.001
+  echo "set AMP_Scale_Factor = ${AMP_Scale_Factor}" >> LOGS/${scriptname}.results
+  ${proc_2dx}/linblock "WARNING: AMP_Scale_Factor corrected to ${AMP_Scale_Factor}"
+endif
+# 
 if ( ${MergeAK}x == 'x' ) then
   set MergeAK = "10"
   echo "set MergeAK = ${MergeAK}" >> LOGS/${scriptname}.results

kernel/2dx_merge/scripts-standard/2dx_finalmerge.script

@@ -59,6 +59,7 @@
 # DISPLAY: scalimamp3d_rref
 # DISPLAY: scalimamp3d_BXYMINMAX
 # DISPLAY: scalimamp3d_BZMINMAX
+# DISPLAY: AMP_Scale_Factor
 # DISPLAY: scalimamp3d_BEXTRA
 #
 #$end_local_vars
@@ -104,6 +105,7 @@ set MergeIWP = ""
 set MergeLatLine_MaxAmpFactor = ""
 set MergeLatLine_REDUCAC = ""
 set max_amp_correction = ""
+set AMP_Scale_Factor = ""
 set merge_ML_data = ""
 set plotres_rings = ""
 set lattice = ""
@@ -159,6 +161,12 @@ if ( `echo ${RESMIN} ${RESMAX} | awk '{ if ( $1 < $2 ) { s = 1 } else { s = 0 }}
   echo "set RESMAX = ${RESMAX}" >> LOGS/${scriptname}.results
 endif
 #
+if ( ${AMP_Scale_Factor}x == ‘x’ ) then
+  set AMP_Scale_Factor = 0.001
+  echo "set AMP_Scale_Factor = ${AMP_Scale_Factor}" >> LOGS/${scriptname}.results
+  ${proc_2dx}/linblock "WARNING: AMP_Scale_Factor corrected to ${AMP_Scale_Factor}"
+endif
+# 
 if ( ${MergeAK}x == 'x' ) then
   set MergeAK = "10"
   echo "set MergeAK = ${MergeAK}" >> LOGS/${scriptname}.results

kernel/2dx_merge/scripts-standard/2dx_generateImageMaps.script

@@ -13,7 +13,7 @@
 #                                                                           #
 #############################################################################
 #
-# SORTORDER: 70
+# SORTORDER: 92
 #
 # MANUAL: This script makes use of MRC and CCP4 commands to generate the projection maps of all selected images, using the latest phase origin settings.
 #

kernel/2dx_merge/scripts-standard/2dx_merge.script

@@ -53,6 +53,7 @@
 # DISPLAY: Merge_Reference_HKMAX
 # DISPLAY: MergeAK
 # DISPLAY: MergeIWF
+# DISPLAY: AMP_Scale_Factor
 # DISPLAY: MergeIWP
 # DISPLAY: MergeLatLine_MaxAmpFactor
 # DISPLAY: MergeLatLine_REDUCAC
@@ -84,6 +85,7 @@ set realang = ""
 set ALAT = ""
 set SYM = ""
 set merge_ref_num = ""
+set AMP_Scale_Factor = ""
 set avrgamphsNUMBER = ""
 set avrgamphsRESOL = ""
 set ILIST = ""
@@ -244,6 +246,12 @@ endif
 #
 echo "<<@progress: 5>>"
 #
+if ( ${AMP_Scale_Factor}x == ‘x’ ) then
+  set AMP_Scale_Factor = 0.001
+  echo "set AMP_Scale_Factor = ${AMP_Scale_Factor}" >> LOGS/${scriptname}.results
+  ${proc_2dx}/linblock "WARNING: AMP_Scale_Factor corrected to ${AMP_Scale_Factor}"
+endif
+# 
 if ( ${MergeAK}x == 'x' ) then
   set MergeAK = "10"
   echo "set MergeAK = ${MergeAK}" >> LOGS/${scriptname}.results

kernel/2dx_merge/scripts-standard/2dx_mergeRefine.script

@@ -45,6 +45,7 @@
 # DISPLAY: MergeHKMAX
 # DISPLAY: Merge_Reference_HKMAX
 # DISPLAY: MergeLatLine_REDUCAC
+# DISPLAY: AMP_Scale_Factor
 # DISPLAY: ILIST
 # DISPLAY: MergeIPAT
 # DISPLAY: MergeDELPLT
@@ -107,6 +108,7 @@ set realang = ""
 set ALAT = ""
 set MergeStepSize = ""
 set IBOXPHS = ""
+set AMP_Scale_Factor = ""
 set SYM = ""
 set avrgamphsNUMBER = ""
 set avrgamphsRESOL = ""
@@ -221,6 +223,12 @@ if ( `echo ${RESMIN} ${RESMAX} | awk '{ if ( $1 < $2 ) { s = 1 } else { s = 0 }}
   echo "set RESMAX = ${RESMAX}" >> LOGS/${scriptname}.results
 endif
 #
+if ( ${AMP_Scale_Factor}x == ‘x’ ) then
+  set AMP_Scale_Factor = 0.001
+  echo "set AMP_Scale_Factor = ${AMP_Scale_Factor}" >> LOGS/${scriptname}.results
+  ${proc_2dx}/linblock "WARNING: AMP_Scale_Factor corrected to ${AMP_Scale_Factor}"
+endif
+# 
 if ( ${MergeAK}x == 'x' ) then
   set MergeAK = "10"
   echo "set MergeAK = ${MergeAK}" >> LOGS/${scriptname}.results

kernel/config/2dx_master.cfg

@@ -2821,6 +2821,18 @@ set Merge_Reference_HKMAX = "20"
 # USERLEVEL: SIMPLE
 set ILIST = "y"
 #
+# LABEL: AMP_Scale_Factor
+# LEGEND: Defines a down-scaling factor to reduce the AMPLITUDES and also the BACKGROUND measurements in the dataset. This may be needed to make sure the values for SIGF stay below 999.0, which is the signal for invalid measurements.  You could use a AMP_Scale_Factor value of 0.001.
+# EXAMPLE: AMP_Scale_Factor = 0.001
+# HELP: http://2dx.org/documentation/2dx-software/parameters/Merging
+# TYPE: Float "MIN=0.0;MAX=1.0;DEFAULT=0.001"
+# LOCKED: YES
+# INHERITABLE_UPON_INIT: YES
+# SYNC_WITH_UPPER_LEVEL: NO
+# USERLEVEL: ADVANCED
+# ISWRONG: YES
+set AMP_Scale_Factor = "0.001"
+#
 # LABEL: MergeAK
 # LEGEND: Defines the relative weights for phases with respect to amplitudes, for lattice line generation. If your Defocus is determined very precisely, then the Thon rings are well placed and the amplitudes are more reliable. In that case, you can use a smaller value (e.g. 2.0). If the defocus values are not too reliable, then a larger value of 3.0 or 4.0 might work better.
 # EXAMPLE: MergeAK = 3.0

kernel/mrc/source/2dx_latlinek.for

@@ -666,7 +666,17 @@ C
           FMERIT = ABS(COS(AMIN1(ABS(SIGPHI(J)),90.0)/CNV))
           if(FMERIT.lt.0.00001)FMERIT=0.0
 
-          if(SIGF(J).gt.99998)then
+CHEN>  
+C          if(FMERIT.lt.0.5 .or. NOBS.le.8 .or.abs(SIGF(J)).gt.99998.0)then
+C            F=0.0
+C            FOUT(J)=0.0
+C            SIGF=0.0
+C            SIGF(J)=0.0
+C            FMERIT=0.0
+C            SIGOUT=100.0
+C          endif
+CHEN<
+          if(abs(SIGF(J)).gt.99998)then
             FMERIT=0.0
             SIGOUT=100.0
           endif
@@ -709,28 +719,34 @@ CHENN>
 C95     WRITE(6,4000) NPRO,NPROMX
 95      WRITE(6,4000) NPROF,NPROMX
 CHENN<
-        GOTO 99
+        GOTO 991
 96      WRITE(6,4100) NOBS,NOBSMX
-        GOTO 99
+        GOTO 991
 97      WRITE(6,4200) NCALC,NCALMX
-        GOTO 99
+        GOTO 991
 98      WRITE(6,4300) NPLT,NPLTMX
-4000    FORMAT(/,/,' TOO MANY POINTS IN PROFILE!!    FOUND= ',I8,
+        GOTO 991
+4000    FORMAT(/,/,':: TOO MANY POINTS IN PROFILE!!    FOUND= ',I8,
      .  ' MAX= ',I8)
-4100    FORMAT(/,/,' TOO MANY OBSERVED DATA POINTS!! FOUND= ',I8,
+4100    FORMAT(/,/,':: TOO MANY OBSERVED DATA POINTS!! FOUND= ',I8,
      .  ' MAX= ',I8)
-4200    FORMAT(/,/,' TOO MANY LATTICE POINTS!!       FOUND= ',I8,
+4200    FORMAT(/,/,':: TOO MANY LATTICE POINTS!!       FOUND= ',I8,
      .  ' MAX= ',I8)
-4300    FORMAT(/,/,' TOO MANY POINTS TO PLOT!!       FOUND= ',I8,
+4300    FORMAT(/,/,':: TOO MANY POINTS TO PLOT!!       FOUND= ',I8,
      .  ' MAX= ',I8)
+
 C               Output of overall statistics
-99      WRITE(6,4400) NFSUM,NPSUM,RFSUM/NFSUM,RMSPSUM/NPSUM,
-     .          WRFSUM/WSUMSUM,SQRT(WRMSPSUM/WNPSUM)
 CHENN>
+99      continue
         OPEN(UNIT=17,FILE='latline.statistics',STATUS='NEW')
         WRITE(17,4400) NFSUM,NPSUM,100.0*RFSUM/NFSUM,RMSPSUM/NPSUM,
      .          100.0*WRFSUM/WSUMSUM,SQRT(WRMSPSUM/WNPSUM)
         CLOSE(17)
+991     continue
+C-------Skip writing the above latline.statistics file, 
+C-------to produce a crash to notice the problem in this program.
+        WRITE(6,4400) NFSUM,NPSUM,RFSUM/NFSUM,RMSPSUM/NPSUM,
+     .          WRFSUM/WSUMSUM,SQRT(WRMSPSUM/WNPSUM)
 CHENN<
 4400    FORMAT(/,' Overall statistics :',/,
      .  '               Number of amplitudes observed==========',I8,/,
@@ -1043,7 +1059,11 @@ C
 1001  FORMAT(' Scale factor= ',G14.5,/)
 C
       IF (IFLAG.EQ.0) GOTO 90 
-      IF (D .LT. 1.E-30) WRITE(6,2002) 
+CHEN>
+      if (D .LT. 1.E-30) then
+        WRITE(6,2002) 
+      endif
+CHEN<
 2002  FORMAT(/,' ********** WARNING DETERMINANT NEAR ZERO : ',
      .' SIGMAS CALCULATED FOR THIS LINE, BUT SUSPECT !!! *****')
 
@@ -2030,10 +2050,6 @@ C
 CHEN>
       ZMM=ZRANG*ZMAG
       ZMAGlocal=ZMAG
-      write(6,'(''XPLTSIZ='',F12.3)')XPLTSIZ
-      write(6,'(''YPLTSIZ='',F12.3)')YPLTSIZ
-      write(6,'(''ZMIN,ZMAX='',2F12.3)')ZMIN,ZMAX
-      write(6,'(''ZMM,ZMAG='',2F12.3)')ZMM,ZMAG
 6     continue
       ZMMlocal=ZRANG*ZMAGlocal
       IF (ZMMlocal .GT. 75.0) GOTO 7
@@ -2043,7 +2059,6 @@ CHEN>
 CHEN<
 7     continue
       ZERO=-ZMIN*ZMAG
-      write(6,'(''ZERO='',F12.3)')ZERO
 C
 C  DRAW AXES FOR AMPLITUDE BOX
 C

kernel/mrc/source/2dx_latlinprescal.for

@@ -82,6 +82,14 @@ C
           RMAXVAL=1.0
           write(*,'(''This is corrected to= '',F12.1)')RMAXVAL
         endif
+C
+      write(*,'(/,''Give Scale Factor to downscale AMP and BCK (e.g. 0.001):'')')
+      READ(5,*)RSCALEFAC
+      if(RSCALEFAC.lt.0.000001)RSCALEFAC=0.001
+      if(RSCALEFAC.gt.1.0)RSCALEFAC=1.0
+      write(*,'(''Scale Factor for AMPlitudes and BACKground values is '',F16.9)')
+      write(*,'(''Use this to make sure that the SIGF values stay below 999.0'')')
+      write(*,'(''so that errors can be encoded with that number'')')
 C
       NPASS=0
       NOUT=0
@@ -98,6 +106,11 @@ C
       READ(czeile,*,ERR=18)
      1 IHM,IKM,ZM,AMP,PHASE,IFILM,IQ,WTFACTOR,BCK,CTF
 C
+CHEN>
+      RSCALEFAC=0.0001
+      AMP=AMP*RSCALEFAC
+      BCK=BCK*RSCALEFAC
+CHEN<
 C       write(*,'('' read: '',2I,3F,2I,3F)')
 C      1 IHM,IKM,ZM,AMP,PHASE,IFILM,IQ,WTFACTOR,BCK,CTF
 C

kernel/proc/2dx_merge_latline_sub.com

@@ -100,16 +100,17 @@ eot
   echo "1001,${zminmax} ! NSER,ZMIN,ZMAX " >> LOGS/latlinprescal.log
   echo "${MergeIQMAX}               ! IQMAX " >> LOGS/latlinprescal.log
   echo "${max_amp_correction}       ! Max_Amp_Correction" >> LOGS/latlinprescal.log
+  echo "${AMP_Scale_Factor}         ! AMP_Background_Scale Factor" >> LOGS/latlinprescal.log
   echo "eot " >> LOGS/latlinprescal.log
   echo " " >> LOGS/latlinprescal.log
   echo "Running: " >> LOGS/latlinprescal.log
   echo "======== " >> LOGS/latlinprescal.log
   #
-  #
   ${bin_2dx}/2dx_latlinprescal.exe << eot >> LOGS/latlinprescal.log
 1001,${zminmax} ! NSER,ZMIN,ZMAX
 ${MergeIQMAX}               ! IQMAX
 ${max_amp_correction}       ! Max_Amp_Correction
+${AMP_Scale_Factor}         ! AMP_Background_Scale Factor
 eot
   #
   \rm -f fort.1
@@ -206,6 +207,7 @@ echo "${MergeIGUESS},${MergeBINSIZ}                       # IGUESS,BINSIZ"
 echo "${MergeNCYCLS},${MergeMPRINT}                          # NCYCLS,MPRINT"
 echo "${idoh},${idok}		                          # H,K indices to plot. 0 0 = all."
 echo "${IAQP2},${iplterr},${imaxIQplot}                         # IAQP2: 1=y,0=n, iplterr=1:errbar in PHS, maxIQ for PSplot"
+echo "${RMAXAMP}"
 echo " "
 #
 ${bin_2dx}/2dx_latlinek.exe << eot > LOGS/2dx_latlinek.log