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Re: [ccp4bb]: calculate anomalous difference (map)
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Cheng Yang wrote:
>
> Does anyone know any program can calculate the anomalous difference
> using a PDB and HKL file? Thanks.
>
The anomalous differences should be in your HKL file. I assume
you want to calculate a phased anomalous difference map.
Make sure the HKL file has anomalous differences preserved.
And that the pdb file is for the structure in that same crystal,
so that it can be used for phasing the data without doing
molecular replacement.
Then:
scalepack2mtz (or whatever it takes to get your hkl into mtz format)
truncate (to get an .mtz file with Fp (and preferably sigfp))
sfall (to calculate structure factors and add them to your mtz)
mode sfcalc xyzin hklin
fft (to calculate the map)
LABIN DANO=DANO SIG1=SIGDANO PHI=PHIC
-----------------
below are approximate command files for doing this,
the documentaion has more.
scalepack2mtz hklin chad11_ano.sca \
hklout i.mtz << eof
!cell 121.327 43.255 55.336 90.000 97.186 90.000
SYMM 19
END
eof
truncate hklin i.mtz hklout chad11a.mtz <<EOF-trunc
title -
!nresidues 4200
!labout F=FP SIGF=SIGFP
EOF-trunc
setenv MEMSIZE 3000000
sfall XYZIN structure.pdb hklin chad11a.mtz \
HKLOUT sfall.mtz << END-sfall
TITL calc sf's from model
MODE sfcalc xyzin hklin
labin FP=FP SIGFP=SIGFP F9=DANO F10=SIGDANO
labout FC=FC PHIC=PHIC
#RESOLUTION 25.0 3.2
BINS 60
RSCB 3.0 2.1
BRESET 1.0
END
END-sfall
fft \
hklin sfall.mtz \
mapout anodif.map \
<<EOF-fft
TITLE chd ano fft map
LABIN DANO=DANO SIG1=SIGDANO PHI=PHIC
resolution 999. 3.0
EOF-fft
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