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Re: [ccp4bb]: calculate anomalous difference (map)
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To vary the B-factor,
In the final fft script, add the following line:
SCALE F1 1.0 -20.0
vary the last number (-20) which is the B-factor.
A negative means sharpening, positive is blurring.
You can also vary the resolution limit to get a similar type
of information. If the high resolution phases and/or ano
differences are no good, the high resolution only adds noise
and the peak heights will be greater with limited resolution.
In that case B-factor sharpening will make the map worse,
a positive B-factor will make it better.
(all this assuming the HKL file contains actual experimental
anomalous differences)
If you want to vary the B-factor of the anomalous scatterer
in the PDB file and see the effect on anomalous peak height,
you need to calculate the anomalous differences as well as
phases from the pdb file. I don't know if sfall knows about
anomalous scatterers. My instructions don't apply.
Cheng Yang wrote:
>
> 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
>>