(mtz data files and scripts for this
example are on hermione in
/home/dave/ccp4_examples)
Start with 4 mtz files:
L9 native data
= e100c_nat3.mtz
L9 iodine
derivative = e100c3i.mtz
L9 Hg derivative
#1 = thim.mtz
L9 Hg derivative
#2 = pcmb4.mtz
1) Merge
the 4 mtz files into one mtz file using CAD
using the
script "cad_L9.sh". The output mtz file containing
all 4 data
sets is called "L9_merge.mtz".
2) Scale
the 4 data sets using SCALEIT using the script "scaleit.sh"
The scaled
mtz file is called "L9_merge_scale.mtz".
3) Use mlphare
to do the phase calculation, using the script "mlphare_L9.sh".
The output
mtz file with the new phases is called "L9_phase_mir.mtz".
4) Use DM
to do solvent flattening, and FFT to calculate an electron density map.
The script
to do both of these is called "L9_solflt.sh".
The output
electron density map is called "L9_solflt.map".
Solvent flattened MIR map calculated in this example using CCP4
==================================================
Here are the CCP4 scripts:
1) cad_L9.sh:
#!/bin/sh
cad
\
HKLIN1 e100c_nat3.mtz
\
HKLIN2 e100c3i.mtz
\
HKLIN3 thim.mtz
\
HKLIN4 pcmb4.mtz
\
HKLOUT L9_merge.mtz
\
<< END-cad
LABIN FILE
1 E1=Fnat E2=Snat
LABIN FILE
2 E1=Fiod E2=Siod
LABIN FILE
3 E1=Fthim E2=Sthim
LABIN FILE
4 E1=Fpcmb4 E2=Spcmb4
Title L9 native, iod, thim, pcmb, merged data
END
END-cad
#
======================================================
2) scaleit.sh:
#!/bin/sh
set -e
scaleit
\
HKLIN L9_merge.mtz
\
HKLOUT L9_merge_scale.mtz
\
<< END-scaleit
TITLE FPHs
scaled to FP
reso 90 2.2
refine isotropic
LABIN FP=Fnat
SIGFP=Snat -
FPH1=Fiod
SIGFPH1=Siod -
FPH2=Fthim
SIGFPH2=Sthim -
FPH3=Fpcmb
SIGFPH3=Spcmb
CONV ABS 0.0001 TOLR 0.000000001 NCYC 4
END
=======================================================
3) mlphare_L9.sh:
#!/bin/sh
set -e
mlphare HKLIN L9_merge_scale.mtz
\
HKLOUT L9_phase_mir.mtz \
<< eof-phare
TITLE Phasing of L9 with mlphare
using Iodine and Hg derivatives
RESO 95.0 2.2
CYCLE 10
ANGLE 10
LABIN FP=Fnat SIGFP=Snat
-
FPH1=Fiod
SIGFPH1=Siod -
FPH2=Fthim
SIGFPH2=Sthim -
FPH3=Fpcmb
SIGFPH3=Spcmb
LABOUT ALLIN
FHOUT DERIV 1 2 3
DERIV iod
DCYCLE PHASE ALL REFCYC ALL
KBOV ALL
RESO 90.0 2.4
ATOM I
0.053 0.188 0.206 1.000 BFAC
25.000
ATREF X ALL Y ALL Z ALL #
OCC ALL
ATOM I
0.064 0.233 0.132 1.000 BFAC
25.000
ATREF X ALL Y ALL Z ALL #
OCC ALL
DERIV thim
DCYCLE PHASE ALL REFCYC ALL
KBOV ALL
RESO 90.0 2.4
ATOM HG
0.918 0.049 0.235 1.000 BFAC 25.000
ATREF X ALL Y ALL Z ALL #
OCC ALL
DERIV pcmb
DCYCLE PHASE ALL REFCYC ALL
KBOV ALL
RESO 90.0 2.4
ATOM HG
0.917 0.052 0.230 1.000 BFAC 25.000
ATREF X ALL Y ALL Z ALL #
OCC ALL
END
eof-phare
#
============================================
4) L9_solflt.sh:
#! /bin/sh
set -e
dm hklin L9_phase_mir.mtz hklout
L9_phase_solflt.mtz \
solout $CCP4_SCR/solvent.msk
<<+
solc 0.55
mode solv hist mult
NCYC AUTO
SCHEME ALL
COMBINE OMIT SETS 10
LABIN FP=Fnat SIGFP=Snat PHIO=PHIB
FOMO=FOM
LABOUT PHIDM=PHI1 FOMDM=W1
+
# Calculate map from density modified map.
fft hklin L9_phase_solflt MAPOUT
L9_solflt.map << +
TITLE Map from solvent flattening
reso 90.0 2.2
XYZLIM 0.0 1.0 -0.2 0.5 0.0
1.0
LABIN F1=Fnat SIG1=Snat PHI=PHI1
W=W1
END
#
============================================
