This may also be a job for 'convert2mtz', which I think will pick up the
complex columns automatically. Only available from the command line though.
Kevin
Eleanor Dodson wrote:
> I am no expert on CNS files, but do the entries for F_BULK and F_MODEL
> correspond to an amplitude and a phase - it certainly looks like that..
>
> If so you can read both in:
>
> I havent checked the format but your script would look like this
>
> title [No title given]
> format
> '(6X,3F5.0,6X,F10.0,6X,F10.0,6X,F10.0,/,25X,F10.0,6X,F10.0,7X,2F10.0,/,28X,F10.0,10X,F10.0,10X,F10.0,/,28X,F10.0,11X,F10.0,/,27X,2F10.0)'
>
> skipline 5
> labout H K L IP SIGIP FP SIGFP FreeRflag Fbulk PHIbulk HLA HLB HLC HLD
> FOM Fcalc PHIcalc
> ctypout H H H J Q F Q X F P A A A A W F P
> PNAME tony
> DNAME z
> XNAME x
> end
>
>
> Miriam Sharpe wrote:
>> Hi everyone,
>>
>> I've been looking at ways to convert an old hkl file from a CNS
>> refinement (see details below) into an mtz file.
>>
>> F2mtz in ccp4 will do this once I have told it the fortran format of
>> the hkl file (below), and specified the data type and label for the
>> input fields.
>>
>> However, I'm not sure how to define the F-MODEL and FBULK columns in
>> terms of mtz column types. Both are two-part columns containing
>> complex Fcalc with both amplitude and phase information.
>> Any suggestions are most welcome!
>>
>> Thanks,
>> Miriam Sharpe
>>
>> Dr Miriam L Sharpe
>> Postdoctoral Fellow
>> Department of Biochemistry University of Otago
>> PO Box 56
>> 710 Cumberland St
>> Dunedin 9054 , New Zealand
>> _______________________________________________________________
>> the list of columns in the hkl file:
>>
>> IOBS=experimental intensity from .sca file
>> SIGI=sigma of IOBS
>> FOBS=square root of IOBS
>> SIGMA=sigma of FOBS
>> TEST=Rfree flag
>> FBULK=bulk solvent part of Fcalc
>> PA_MODEL = HL coeff.
>> PB_MODEL= HL coeff.
>> PC_MODEL = HL coeff.
>> PD_MODEL = HL coeff.
>> FOM_MODEL =figure of merit
>> F_MODEL = complex Fcalc, includes both amplitude and phase
>>
>> and the first two reflection entries:
>>
>> INDE 38 21 4 IOBS= 771.500 SIGI= 1140.300 FOBS= 27.780
>> SIGMA= 27.780 TEST= 0 FBULK=
>> 0.333 55.023
>> PA_MODEL= 5.685 PB_MODEL= 5.558
>> PC_MODEL= 0.000
>> PD_MODEL= 0.000 FOM_MODEL= 0.935
>> F_MODEL= 135.595 44.354
>> INDE 38 21 3 IOBS= 18.500 SIGI= 861.100 FOBS= 4.300
>> SIGMA= 4.300 TEST= 0 FBULK=
>> 0.542 82.489
>> PA_MODEL= 1.334 PB_MODEL= 0.159
>> PC_MODEL= 0.000
>> PD_MODEL= 0.000 FOM_MODEL= 0.555
>> F_MODEL= 147.826 6.802
>>
>> Corresponding Fortran format (I think):
>> (6X,3F5.0,6X,F10.0,6X,F10.0,6X,F10.0,/,25X,F10.0,6X,F10.0,7X,2F10.0,/,28X,F10.0,10X,F10.0,10X,F10.0,/,28X,F10.0,11X,F10.0,/,27X,2F10.0)
>>
>>
>>
>> MTZ Column Types:
>> H
>> index h,k,l
>> F
>> structure amplitude, F
>> D
>> anomalous difference
>> Q
>> standard deviation of anything: J,F,D or other
>> P
>> phase angle in degrees
>> W
>> weight (of some sort)
>> A
>> phase probability coefficients (Hendrickson/Lattmann)
>> B
>> BATCH number
>> S
>> 1/d**2 = 4 (sin theta/lambda)**2
>> J
>> intensity
>> Y
>> M/ISYM, packed partial/reject flag and symmetry number
>> I
>> any other integer
>> R
>> any other real
>> U
>> partial FC (see CAD)
>> V
>> partial PHIC (see CAD)
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