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Re: [ccp4bb] hkl into mtz using f2mtz |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: hkl into mtz using f2mtz From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2010-02-18 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) CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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