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

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Cheng Yang wrote:
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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
> 
> 


  Have you got the whole structure coorstinates?

  If so, calculate FC PHIC FOM from that - refmac5 will output these to 
a file

  Then do a map
fft - anom differenc map
  DANO = DANO_data PHI=PHIC W=FOM

  followed by a peak search.

  It all can be done very easily within the GUI

  Then you will have to check whether your peaks are where you expect 
them to be - over the anom scatterers..

  But there is a big problem with the interaction between noise and 
signal and resolution. ( very little influence actually from the B 
factors of the model - more important is the quality of the refinement. 
Obv. the FOM goes up as the R factor comes down)

  You ca use this technique to decide at what resolution your anom 
signal becomes valueless - if the highest peaks are not the ano 
scatterers your  anom diffs are probably actually random noise..)

  Eleanor


> 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
>>
>>
>>
>>--
>>
>>
> 
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