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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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