Re: [ccp4bb]: calculate anomalous difference (map)

[Cheng Yang <cyang@msc.com>]

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   I may not explain myself clearly. What I need to do is to see the
difference of anomalous peaks height using the PDB with different
B-factors.

  Cheng


On Tue, 1 Apr 2003, Edward Berry wrote:

>
>
> 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
>
>
>
> --
>
>