Using electron density as a MR model-

Note this script is not runnable- it needs editing as to
names of input files, space group, cell parameters etc.
But it has example scripts of all the steps.

Steps 1-3 are to generate the density of a single
copy of the model (which could be a dimer or trimer if 
 that is what you want to use for the model, ie the same
 multimer is expected in the target cell as well). 
 in a P1 cell of dimensions large enough that 
 cross-vectors between monomers are excluded.
 
If you already have a density map with a single copy, 
you can use that directly in step 4.

(Steps 1-3 could be done with mapmask rather than mapman/mave)


# Input files- (1-5 are just for generating the density map to be used as model)
1. oldphs.mtz - phased mtz file for making map of solved crystal
2. dimref.msk Mask around density of one monomer (or multimer) in phased crystal
3. ref2old.o - operator taking density in known cell to ref cell- use unit op 
   if mask is in phased cell in which case ref cell is same as phased cell. 
4. space group operators for phased cell and for P1 symmetry
6. newxtal.mtz- unphased data from new crystal
#------------------------


#1. Make large p1 cell as template for MAVE:
## this could be done directly with mapman (or mapmask?).
# density will be put in this cell for SF calculation:

# phony mtz file for template:
echo '   0   3   4  2741.    90.' > junk.rfl
f2mtz   HKLIN junk.rfl \
	HKLOUT blank300.mtz <<eof
title arbitrary sf's for making map with arbitrary cell etc.
cell  =   300. 300. 300.  90.  90.  90.
SYMMETRY 1
labOUT H K L FP PHIC 
CtypeOUT  H H H F P 
FORMAT '(3F4.0,4F8.2)'
SKIP 2
END
eof
#FFT1.COM;5                  1  23-JUN-1995 17:06:20.05
fft hklin blank300.mtz mapout blank300.map <<EOF-fft
TITLE arbitrary map for template
LABIN  F1=FP  PHI=PHIC
  SCALE F1 100.0 0.0
!cell 300 300 300 90 90 90
GRID   160  160 160
EOF-fft
#---------------------------------------------

# 2. make map of the density to be used:
# e.g. mir map of phased crystal

#FFTold:
fft \
 hklin oldphs.mtz \
 mapout temp.map \
 <<EOF-fft
TITLE  map from 
fftspacegroup 1
LABIN  F1=FP W=FOM PHI=PHIB
  SCALE F1 1.000 0.0
GRID   160 160  240
XYZLIM 0 161 0 161 0 62 
EOF-fft
#--------------------------------
#use mapmask- extend is obsolete
# extend fft map to 1 asu plus 1 or 2 pixels to satisfy MAVE:
extend MAPIN temp.map MAPOUT old1.map << END-extend
XYZLIM 0 162 0 162 0 62
symm 19
END-extend
#--------------------------------

3. MAVE to average the density (or just cut it out if no NCS) 
# and expand it into large 300x300x300 cell:
# (may have to remove comments from lines to run it)
#AVEold:
#mave to make map with dimer density inside mask
mave -b <<eof-1
ave
old1.map
ref.msk     !mask to be used
ref2old.o   !unit operator is ok- define ref cell same as real
p212121.o   !space group operators for solved crystal
unit.o      ! first ncs operator always present- 
ncsold.o    ! 2nd ncs op- delete this line if no NCS in solved crystal

oldz160.map ! Template for averaged map- 
old2.map    ! name for averaged map
eof-1
#---------------------------------------------------

#---------------------------------------------
##Expand mir density into large p1 cell for rotation function:
#chc2.map made by averaging (solvent flattening) mir map
mave -b <<eof-1
exp
old2.map
dimref.msk
unit.o
p1.o
p1.o
unit.o

blank300.map  ! template for expanded map
old-300.map   ! name for expanded map
eof-1



#4. calculate structure factors from density expanded into large P1 cell:
#############################
#SFALL in space group P1:
sfall \
       mapin   old-300.map \
       hklout  old-300.mtz  \
<< END-sfall
TITL Calc Fc's from ave'd dimer in 300A cell for RF ALMN
MODE SFCALC mapin 
RESO 999.  3.8
symm 1
SFSG 1
LABI FP=FP SIGFP=SIGFP
LABO FC=FC PHIC=PHIC
END
END-sfall
#--------------------------------------

#NOW YOU CAN USE (ALMN + TFFC) OR AMORE. 
#amore is easier- there is no reason to use ALMN + TFFC.

#---------------------------------------------
#AMORE procedure:

#--------------------------------------
#5.    sorting run:  for MODEL structure factors (phased).
#    this takes the place of TABLING in an ordinary amore run
#   #############  note keyword "model". produce .tab
#
#  mtz file contains cell and symmetry.
amore SORTING_NR 1000000 \
   hklin old300.mtz  \
  table1 model.tab  <<  eof
TITLE   ** xxxx**
SORTFUN model 45 4.0
LABI FC=FC  PHIC=PHIC 
eof
#---------------------------------------------


#6.    sorting run:  for new crystal data (unphased)
#   #############
#
#  mtz file contains cell and symmetry.
amore hklin newxtal.mtz  \
hklpck0 data.hkl <<  eof
TITLE   ** xxxx**
SORTFUN RESOL 45 4.0
LABI FP=FP  SIGFP=SIGFP
eof
#---------------------------------------------

#------------------------------------------
#7.    roting run:
#   #############   comb.tab from combined averaged density in ref orient
####                                                   in 300A cube cell
       
amore  TABLE1 /a/mave-bbc/model.tab    \
 HKLPCK1 model.hkl   \
 hklpck0 data.hkl  \
 clmn1 model.clmn    \
 clmn0 data.clmn   \
 MAPOUT amore_cross.map \
       ROTING_MI 1100000     \
       ROTING_MR  9200000   \
       ROTING_MC  9000000   \
         <<eof
ROTFUN
VERB
TITLE : Generate HKLPCK1 from MODEL FRAGMENT   1
GENE 1   RESO 45.0 4.5 CELL_MODEL 250 250 250
CLMN MODEL 1  FLIM 0. 1.E8    RESO  45 4.5 SPHERE  50
CLMN CRYSTAL ORTH  1 FLIM 0 1.E8  SHARP 0.0 RESO  45 4.5 SPHERE  50
ROTA  CROSS  MODEL 1  BESLIMI 3 200 STEP 1.5 PKLIM 0.2  NPIC 100
eof

                                          axis type B at 90*, 1/6

#
#8.   tra-ing run:
#   #############
#
amore  TABLE1 /a/mave-bbc/model.tab \
       HKLPCK0 data.hkl \
       MAPOUT amore_transjunk1.map \
       TRAING_MEQ 6    \
       TRAING_NR   30000    \
       TRAING_MT  8100000   \
      TRAING_MRT  5807543    \
      >! trans.log << eof
TRAFUN CB   NMOL 1 RESO 45 6.2  PKLIM 0.5  NPIC 10
SYMM P212121
!HKLM 219 219 219 25
VERB
TITLE : Translation function
CRYSTAL ORTH  1 FLIMI 1.E1 1.E8   SHARP 0.0
 SOLUTIONRC    1   30.33   31.87  243.26  0.0000  0.0000  0.0000 46.1 53.0 60.6 29.0   1
 SOLUTIONRC    1   30.35   31.88   63.24  0.0000  0.0000  0.0000 46.1 53.0 60.5 29.1   2
eof
grep SOLUTIONTF trans.log > trans.sol
#############
#9     FIT-ing

#FITTING 
amore  TABLE1 /a/mave-bbc/model.tab \
       FITING_MEQ   4    \
       FITING_NR 260000    \
       FITING_MT 8100000 \
        HKLPCK0 data.hkl >! fit.log <<eof
FITFUN  NMOL 1  RESO 45 4.2  ITER 20 ! CONV   1.E-3
TITLE *** spmi   structure ***
VERBOSE
CRYSTAL ORTH  1 FLIMI 0.E0 1.E8   SHARP 0.0
SYMM P212121
!HKLM 219 219 219 25
REFSOL   AL     BE   GA     X   Y   Z    BF
 SOLUTIONTF1  1   30.33   31.87  243.26  0.1527  0.4279  0.1584 74.5 35.3 75.7   1  100.0
 SOLUTIONTF1  1   30.35   31.88   63.24  0.1527  0.4278  0.1583 74.3 35.4 75.4   1  100.0
eof
 #############




STOP HERE- below is obsolete.
If you want to use ALMN + TFFC:

#----------------------------------
# 5. Rotation function on unphased crystal:
## FROM THE LOG FILE GET ALPHA, BETA, GAMMA TO MAKE ROTSOL.O
#
# Cross-rotation function
#
almn  hklin /usr11/scratch/berry/data/newxtal.mtz  hklin2 $tmp/old-300.mtz \
  mapout $tmp/almn.map << eof
TITLE
cross 5 46.	
RESOLUTION  999 3.5
CRYSTAL  FILE 1 flimits 4100. 1.e20 ORTHOG 1 BFAC 0
CRYSTAL  FILE 2 flimits 32. 1.e20 ORTHOG 1 BFAC 0
LABIN FILE 1 F=FP
LABIN FILE 2 F=FC
LIMITS 0  180 5
PRINT
FIND  1 30 RMS OUTPUT cross_peaks
END
eof
#


6. select the top rotation peaks, and for each make rot-trans operators
rotsolp61.o (for enantiomorphic space groups do this in both P61 and P65):


#--------------------------------------
#7. NOW GET READY FOR TRANSLATION FUNCTION
#MAKE TEMPLATE OF P1 CELL WITH TARGET CELL PARAM
#f2mtz2:
f2mtz   HKLIN $CCP4_SCR/junk.rfl \
	HKLOUT /temp/berry/temp.mtz <<eof
title arbitrary sf's for making map with arbitrary cell etc.
cell = 212.900  212.900  354.100  90.00  90.00 120.00                          

SYMMETRY 1
labOUT H K L FP PHIC 
CtypeOUT  H H H F P 
FORMAT '(3F4.0,4F8.2)'
SKIP 2
END
eof
#---------------------------------------------
#FFT1.COM;5                  1  23-JUN-1995 17:06:20.05
fft hklin /temp/berry/temp.mtz mapout /temp/berry/rabuc.map <<EOF-fft
TITLE arbitrary map for template
LABIN  F1=FP  PHI=PHIC
  SCALE F1 100.0 0.0
GRID  120  120  200
EOF-fft
#---------------------------------------------
##EXPAND DENSITY INTO P1 CELL WITH TARGET CELL PARAM, CORRECT ROTATION
cd /xray4/berry/almn
/usr11/scratch/berry/rave_sgi/4d_mave -b <<eof-1
exp
/temp/berry/old2.map
../ncs2/ref.msk
rotsolp61.o
../rave/p1.o
../rave/p1.o
../rave/unit.o

/temp/berry/hexuc.map
/temp/berry/rotsolp61.map
eof-1
#############################
sfall \
       mapin   /temp/berry/rotsolp61.map \
       hklout  /temp/berry/rotsolp61.mtz \
<< END-sfall
TITL Calc Fc's from dimer at rot sol orientation in p1 cell
MODE SFCALC mapin
RESO 999.  6.5
SYMM 1
LABI FP=FP SIGFP=SIGFP
LABO FC=FC PHIC=PHIC
END
END-sfall
###############################################
#CAD to combine fobs and P1 fcalc, calculate rotated F's
cad	\
HKLIN1 /usr11/scratch/berry/data/p65.mtz    \
HKLIN2 $tmp/rotsolp61.mtz  \
HKLOUT $CCP4_SCR/tffcin.mtz	\
<< END-cad
# New Cell Over write the MTZ input
RESOLUTION OVERALL 1000 5.
TITLE COMBINING  toxd and rotated domain 1
LABIN FILE 1 E1=FP E2=SIGFP
CTYPIN FILE 1 E1=F E2=Q   

LABIN FILE 2 E1=FC E2=PHIC  
CTYPIN FILE 2 E1=U     E2=V
LABOUT FILE 2 E1=FC    E2=PHIC  
END
END-cad

######################################
#7. TRANSLATION FUNCTION
tffc HKLIN $CCP4_SCR/tffcin.mtz   \
HKLOUT $CCP4_SCR/tffcout.mtz << END
TITLE tffc on hex bc1
RESOLUTION 999. 5.
!SHELLS 0
!POINTGROUP 222
LABIN FP=FP SIGFP=SIGFP  -
FC1=FC1 PC1=PHIC1 FC2=FC2 PC2=PHIC2 -
FC3=FC3 PC3=PHIC3 FC4=FC4 PC4=PHIC4 -
FC5=FC5 PC5=PHIC5 FC6=FC6 PC6=PHIC6 -
#FC7=FC7 PC7=PHIC7 FC8=FC8 PC8=PHIC8 -
#FC9=FC9 PC9=PHIC9 FC10=FC10 PC10=PHIC10 -
#FC11=FC11 PC11=PHIC11 FC12=FC12 PC12=PHIC12 
END
#
#
# ********************************************************************
# *                                                 16/5/91          *
# *   Run FFT  in Space group 1
# *   This is NOT using your real h k l
# *   Resolution limits are artificial; needs to be twice data 
# *   resolution usually.
# *   RESMAX = CELL(1)/"hmax" ( = CELL(2)/"kmax" = CELL(3)/"lmax")
# *   Grid has to be at least 2*"hmax" +1 , etc
# *   TFFC tells you the values of "hmax" etc
# *   Output map should have a single peak giving translation vector.
# *   Asymmetric unit is from one crystal origin to the next (same as RSEARCH)
# *   But do 0-1 , 0-1 0-1 if you feel safer.... and check you have
# *   duplicate solutions.
# ********************************************************************


fft  HKLIN $CCP4_SCR/tffcout.mtz MAPOUT $CCP4_SCR/tffc.map << endfft
RESOLUTION 999. 7.5
! symmetry and fftspacegroup are actually both redundant
SYMMETRY 1
FFTSPACEGROUP 1
TITLE FFT  of tffc map
XYZLIM  0 120 0 120 0 0
GRID      120  120  200
LABIN A=A B=B # actually necessary now
endfft

#exit

# stats on the map:
mapsig mapin $CCP4_SCR/tffc.map mapin2 $CCP4_SCR/tffc.map \
           peak_list $CCP4_SCR/tf.peaks <<eof
!points 1000 
!peaks 100 
eof
#


#----------------------------------
##Now expand with full symmetry into target cell and calculate structure factors: