MIRAS Phasing 
Performing the Calculation with Mlphare from CCP4
Argand Diagram displaying 
the contribution of anomalous scattering 
to the phasing calculation. Taken from a figure from 
Crystallography 101 
MIRAS Phasing:A sample scriptis provided below for a typical MIRAS phasing calculation. All steps on the path are provided from preparing the Scalepack files to displaying the map with O. The general path is:

scalepack2mtz -> 
                truncate -> 
                            cad -> 
                            scaleit -> 
                            mlphare -> 
                                        dm -> 
                                            fft -> 
                                                mapman -> O
 

Example log files are given for each step, along with comments about how to judge the quality of the output. 

Documentation for CCP4 programs:
CCP4 v4.0 Program Documentation locally on /joule2/programs
CCP4 v4.0 Program Documentation from the U.K. site

References for CCP4 programs:
Collaborative Computational Project , Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763 


scalepack2mtz.com
SCRIPT
COMMENTS
#!/bin/csh -f 
#
scalepack2mtz hklin mtz/native.sca \ 
hklout mtz/native_i.mtz <<eof 
SYMM 90 
ANOMALOUS NO 
END 
eof 
#
scalepack2mtz hklin mtz/hg.sca \ 
hklout mtz/hg_i.mtz <<eof 
SYMM 90 
ANOMALOUS YES 
END 
eof 
#
scalepack2mtz hklin mtz/pt.sca \ 
hklout mtz/pt_i.mtz <<eof 
SYMM 90 
ANOMALOUS YES 
END 
eof 
#
scalepack2mtz hklin mtz/pb.sca \ 
hklout mtz/pb_i.mtz <<eof 
SYMM 90 
ANOMALOUS YES 
END 
eof # 
CCP4 document for scalepack2mtz

The native scalepack data set, native.sca, is converted to mtz format first, followed by three derivatives, Hg, Pt, and Pb. 

SYMM -This keyword is compulsory and can be given as the space group name or number. Here we are using space group number 90, otherwise known as P4212. 

ANOMALOUS -Specify whether or not input file contains anomalous data. It is set to NO for the native, and YES for the derivatives. 

---------Logfile from scalepack2mtz---------- 
For each data set check the log file to see that the number of columns, reflections, unit cell, and space group are what you intended. An exerpt from scalepac2mtz on the hg derivative is shown below: 

* Number of Columns = 9 
* Number of Reflections = 19946 
* Column Labels : 
H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) 
* Column Types : 
H H H J Q K M K M 
* Cell Dimensions : 
92.635 92.635 114.259 90.000 90.000 90.000 
* Resolution Range : 
0.00047 0.17361 ( 46.318 - 2.400 A ) 
* Space group = P4212 (number 90) 


truncate.com
SCRIPT
COMMENTS
#!/bin/csh -f 

truncate HKLIN mtz/native_i.mtz \ 
HKLOUT mtz/native_f.mtz \
<< EOF_truncate > log/truncate_native.log 
TITLE native TRUNCATE OUTPUT 
LABOUT F=Fnat sigF=sigFnat 
NRESIDUES 410
EOF_truncate 

truncate HKLIN mtz/hg_i.mtz \ 
HKLOUT mtz/hg_f.mtz \ 
<< EOF_truncate > log/truncate_hg.log 
TITLE Hg TRUNCATE OUTPUT 
LABOUT F=Fhg sigF=sigFhg DANO=Dhg SIGDANO=sigDhg 
NRESIDUES 410 
EOF_truncate 

truncate HKLIN mtz/pt_i.mtz \ 
HKLOUT mtz/pt_f.mtz \ 
<< EOF_truncate > log/truncate_pt.log 
TITLE Pt TRUNCATE OUTPUT
LABOUT F=Fpt sigF=sigFpt DANO=Dpt SIGDANO=sigDpt 
NRESIDUES 410 
EOF_truncate 

truncate HKLIN mtz/pb_i.mtz \ 
HKLOUT mtz/pb_f.mtz \ 
<< EOF_truncate > log/truncate_pb.log 
TITLE Pb TRUNCATE OUTPUT 
LABOUT F=Fpb sigF=sigFpb DANO=Dpb SIGDANO=sigDpb 
NRESIDUES 410 
EOF_truncate 
#
CCP4 document for truncate

The native and derivative data sets are processed with truncate. Truncate converts the intensities into structure factors by taking the square root. Hence, the input files have the extension _i.mtz and the output files have the extension _f.mtz. It also puts the data sets on an absolute scale. This makes it convenient for estimating heavy atom occupancies. 

LABOUT -Output labels for each column of data. These should be meaningful and easy to remember. 

NRESIDUES -The number of residues in the asymmetric unit. Used to put the data sets on an absolute scale. 

---------Logfile from truncate---------- 




Truncate outputs some useful statistics. The Wilson B-factor is calculated and plotted: 

For a wilson plot B = - gradient 
SCALE = exp( - intercept).
Least squares straight line gives: B = 21.434 SCALE = 216.53
where F(absolute)**2 = SCALE*F(observed)**2*EXP(-B*2*SINTH**2/L**2) 
There are also statistics to help you determine whether the data is anisotropic and if there are any systematic absences due to lattice centering.

cad.com
SCRIPT
COMMENTS
#!/bin/csh -f 
#
cad hklin1 mtz/native_f.mtz \ 
hklin2 mtz/hg_f.mtz \ 
hklin3 mtz/pt_f.mtz \ 
hklin4 mtz/pb_f.mtz \ 
hklout mtz/derivs_unscaled.mtz \ 
<log/cad.log
CELL 93.127 93.127 114.335 90.000 90.000 90.000 
RESOLUTION OVERALL 20.0 2.0 
SYMMETRY 90 
TITLE native=pbection, hgote, pt, pbection 
SCAL FILE 1 1.0 
LABIN FILE 1 E1=Fnat E2=sigFnat 
CTYP FILE 1 E1=F E2=Q 
LABOUT FILE 1 E1=Fnat E2=sigFnat 

LABIN FILE 2 E1=Fhg E2=sigFhg E3=Dhg E4=sigDhg 
CTYP FILE 2 E1=F E2=Q E3=D E4=Q 
LABOUT FILE 2 E1=Fhg E2=sigFhg E3=Dhg E4=sigDhg 

LABIN FILE 3 E1=Fpt E2=sigFpt E3=Dpt E4=sigDpt 
CTYP FILE 3 E1=F E2=Q E3=D E4=Q 
LABOUT FILE 3 E1=Fpt E2=sigFpt E3=Dpt E4=sigDpt 

LABIN FILE 4 E1=Fpb E2=sigFpb E3=Dpb E4=sigDpb 
CTYP FILE 4 E1=F E2=Q E3=D E4=Q 
LABOUT FILE 4 E1=Fpb E2=sigFpb E3=Dpb E4=sigDpb 
END 
eof-cad 

CCP4 document for truncate

The native and derivative data sets are processed with truncate. Truncate converts the intensities into structure factors by taking the square root. Hence, the input files have the extension _i.mtz and the output files have the extension _f.mtz. It also puts the data sets on an absolute scale. This makes it convenient for estimating heavy atom occupancies. 

LABOUT -Output labels for each column of data. These should be meaningful and easy to remember. 

NRESIDUES -The number of residues in the asymmetric unit. Used to put the data sets on an absolute scale. 

---------Logfile from truncate---------- 




Truncate outputs some useful statistics. The Wilson B-factor is calculated and plotted: 

For a wilson plot B = - gradient 
SCALE = exp( - intercept).
Least squares straight line gives: B = 21.434 SCALE = 216.53
where F(absolute)**2 = SCALE*F(observed)**2*EXP(-B*2*SINTH**2/L**2) 
There are also statistics to help you determine whether the data is anisotropic and if there are any systematic absences due to lattice centering.

scaleit.com
SCRIPT
COMMENTS
#!/bin/csh -f 
# # scaleit hklin mtz/derivs_unscaled.mtz hklout mtz/derivs.mtz << eof >log/scaleit.log 
TITLE Scaling native and derivatives 
GRAPH H K L MODF 
REFINE ISOTROPIC 
LABI FP=Fnat SIGFP=sigFnat - 
FPH1=Fhg SIGFPH1=sigFhg - 
DPH1=Dhg SIGDPH1=sigDhg - 
FPH2=Fpt SIGFPH2=sigFpt - 
DPH2=Dpt SIGDPH2=sigDpt - 
FPH3=Fpb SIGFPH3=sigFpb - 
DPH3=Dpb SIGDPH3=sigDpb 
eof 
CCP4 document for truncate

The native and derivative data sets are processed with truncate. Truncate converts the intensities into structure factors by taking the square root. Hence, the input files have the extension _i.mtz and the output files have the extension _f.mtz. It also puts the data sets on an absolute scale. This makes it convenient for estimating heavy atom occupancies. 

LABOUT -Output labels for each column of data. These should be meaningful and easy to remember. 

NRESIDUES -The number of residues in the asymmetric unit. Used to put the data sets on an absolute scale. 

---------Logfile from truncate---------- 




Truncate outputs some useful statistics. The Wilson B-factor is calculated and plotted: 

For a wilson plot B = - gradient 
SCALE = exp( - intercept).
Least squares straight line gives: B = 21.434 SCALE = 216.53
where F(absolute)**2 = SCALE*F(observed)**2*EXP(-B*2*SINTH**2/L**2) 
There are also statistics to help you determine whether the data is anisotropic and if there are any systematic absences due to lattice centering.

mlphare.com
SCRIPT
COMMENTS
mlphare HKLIN mtz/derivs.mtz\ HKLOUT mtz/derivs_ph.mtz <log/mlphare.log 
TITLE MAD phasing from acentric data, with four sites + three derivs. 
SYMM 90 
ANGLE 10 
THRESHOLD 2.5 0.5 
PRINT AVF AVE RESO 20 2.0 
EXCLUD SIGFP 3 
CYCLES 20 
LABI FP=Fnat SIGFP=sigFnat - FPH1=Fhg SIGFPH1=sigFhg DPH1=Dhg SIGDPH1=sigDhg - 
                       FPH2=Fpt SIGFPH2=sigFpt DPH2=Dpt SIGDPH2=sigDpt - 
                        FPH3=Fpb SIGFPH3=sigFpb DPH3=Dpb SIGDPH3=sigDpb 
LABO ALLIN PHIB=PHIO FOM=FOMO HLOUT HLA=HLA HLB=HLB HLC=HLC HLD=HLD 
EXCLUDE DISO 590 
EXCLUDE DANO 200 
RUN DERIV Se hg Lambda 0.971139 f' -3 f" 3.5 
DCYCLE PHASE ALL REFCYC ALL KBOV ALL 
ATOM HG 0.386 0.273 0.091 1.000 1.000 BFAC 53.621 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM HG 0.474 0.253 0.114 1.000 1.000 BFAC 29.510 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM HG 0.485 0.255 0.373 1.000 1.000 BFAC 14.148 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM HG 0.217 0.068 0.394 1.000 1.000 BFAC 50.503 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM HG 0.381 0.241 0.115 1.000 1.000 BFAC 23.365 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM HG 0.256 0.088 0.372 1.000 1.000 BFAC 27.015 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
EXCLUDE DISO 430 
EXCLUDE DANO 215 
DERIV Se pt Lambda 0.978680 f' -5.5 f" 4.6 
DCYCLE PHASE ALL REFCYC ALL KBOV ALL 
ATOM PT 0.736 0.114 0.113 1.000 1.000 BFAC 15.807 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM PT 0.250 0.578 0.627 1.000 1.000 BFAC 12.870 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
EXCLUDE DISO 370 
EXCLUDE DANO 270 
DERIV  pb Lambda 0.978437 f' -8.5 f" 2.2 
DCYCLE PHASE ALL REFCYC ALL KBOV ALL 
ATOM PB 0.221 0.444 0.047 1.000 1.000 BFAC 53.986 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM PB 0.366 0.373 0.199 1.000 1.000 BFAC 38.440 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM PB 0.112 0.076 0.285 1.000 1.000 BFAC 35.399 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
ATOM PB 0.121 0.362 0.451 1.000 1.000 BFAC 55.482 
ATREF AX ALL AY ALL AZ ALL OCC 1 3 5 7 9 11 13 15 17 19 AOCC 1 3 5 7 9 11 13 15 17 19 BFAC 2 4 6 8 10 12 14 16 18 20 
END-phare cad 
CCP4 document for truncate

The native and derivative data sets are processed with truncate. Truncate converts the intensities into structure factors by taking the square root. Hence, the input files have the extension _i.mtz and the output files have the extension _f.mtz. It also puts the data sets on an absolute scale. This makes it convenient for estimating heavy atom occupancies. 

LABOUT -Output labels for each column of data. These should be meaningful and easy to remember. 

NRESIDUES -The number of residues in the asymmetric unit. Used to put the data sets on an absolute scale. 

---------Logfile from truncate---------- 




Truncate outputs some useful statistics. The Wilson B-factor is calculated and plotted: 

For a wilson plot B = - gradient 
SCALE = exp( - intercept).
Least squares straight line gives: B = 21.434 SCALE = 216.53
where F(absolute)**2 = SCALE*F(observed)**2*EXP(-B*2*SINTH**2/L**2) 
There are also statistics to help you determine whether the data is anisotropic and if there are any systematic absences due to lattice centering.

dm.com
SCRIPT
COMMENTS
#!/bin/csh -f 
# dm hklin mtz/derivs_ph.mtz hklout mtz/dm.mtz << my-data >log/dm1.log
SOLC 0.55
MODE SOLV HIST MULT
COMBINE OMIT
NCYCLE AUTO
SCHEME ALL
LABIN FP=Fnat SIGFP=sigFnat PHIO=PHIO FOMO=FOMO HLA=HLA HLB=HLB HLC=HLC HLD=HLD
LABOUT PHIDM=PHI1 FOMDM=W1 HLADM=HLADM HLBDM=HLBDM HLCDM=HLCDM HLDDM=HLDDM
my-data 
CCP4 document for truncate

The native and derivative data sets are processed with truncate. Truncate converts the intensities into structure factors by taking the square root. Hence, the input files have the extension _i.mtz and the output files have the extension _f.mtz. It also puts the data sets on an absolute scale. This makes it convenient for estimating heavy atom occupancies. 

LABOUT -Output labels for each column of data. These should be meaningful and easy to remember. 

NRESIDUES -The number of residues in the asymmetric unit. Used to put the data sets on an absolute scale. 

---------Logfile from truncate---------- 




Truncate outputs some useful statistics. The Wilson B-factor is calculated and plotted: 

For a wilson plot B = - gradient 
SCALE = exp( - intercept).
Least squares straight line gives: B = 21.434 SCALE = 216.53
where F(absolute)**2 = SCALE*F(observed)**2*EXP(-B*2*SINTH**2/L**2) 
There are also statistics to help you determine whether the data is anisotropic and if there are any systematic absences due to lattice centering.


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