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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