MTZ2VARIOUS (CCP4: Supported Program)

NAME

SYNOPSIS

DESCRIPTION

KEYWORDED INPUT

OUTPUT, LABIN, END, FSQUARED, MONITOR, RESOLUTION, SCALE, INCLUDE, EXCLUDE, FREEVAL, MISS

OUTPUT [ MULTAN | SHELX | TNT | CIF | XPLOR | CNS | MAIN | SCAL | USER ]

MULTAN

The output file has h, k, l, f, imt in FORMAT(3I4,7X,F7.0,I6), where imt=0 for a good reflection.

SHELX

The output file has the SHELX header followed by all h, k, l, "I", sigma"I", 1 in FORMAT(3I4,2F8.2,I4). Reflections previously excluded from refinement for FreeR analysis are flagged with the word FREE at the end of the line. This means they can be easily extracted from the SHELX file if desired.
NB: The SHELX programs expects intensities, so even if you assign input F terms the program will automatically perform the conversion (see the FSQUARED and SCALE keywords). SHELX is usually used to find heavy atom sites. If FP and FPH are assigned, the program calculates the Diso difference |FP - FPH| and outputs its squared value; |FP - FPH|^2 and an appropriate SIGMA. If you wish to use anomalous differences as input, you can EITHER assign FP=FPH(+) and FPH as FPH(-), which signals the programs to output |FPH(+) - FPH(-)|^2 squared, OR assign DP=DPH in which case the program will output DPH^2.

TNT

The output file has 'HKL ', h, k, l, F, sig(F), phase, fom in format(A4,3I4,3F8.1,F8.4), with phase = 1000, fom = 0 i.e. dummies. Note that files for TNT must be sorted on h, k, l and certain reflection zones are required. You may need to run CAD to resort your data. Use keywords INCLUDE FREER <num> and EXCLUDE FREER <num> to generate files for R-free calculation.
There is a maximum likelihood version of TNT from Pannu and Read which requires a free-R flag (in Xplor convention). This column will be output if you assign the FREE column in LABIN and do not use the INCLUDE | EXCLUDE FREER options.

CIF <data block header>

CIF output is invoked, where <data block header> is a maximum of 80 characters long, and must begin with the characters "data_" (any mixture of upper and lowercase thereafter). OUTPUT CIF can be used to prepare data (from crystallography or EM) for deposition to the PDB.
Unlike the other output formats, all the reflections from HKLIN are written to HKLOUT. Not all column labels are appropriate for CIF output (see Notes on CIF). Also, only RESO, EXCLUDE SIGP and FREEVAL can be used with OUTPUT CIF. They are used to flag certain reflections but not to reject them. The others are ignored.

XPLOR

The output file has FORMAT(A,3I5,A,F10.1,F10.1,A,F10.2,A,I6...). The exact contents will depend on which labels have been specified by the LABIN keyword. See the documentation for FREERFLAG for a table explaining the differences in free R flag conventions.

CNS

Similar to XPLOR output. However, free R flags are left unchanged. To select the correct free R flag in CNS, you will need something like:

{===>} test_flag=0;

Anomalous data

For CIF, SHELX and XPLOR/CNS ONLY. If the anomalous difference is assigned (see LABIN), then the amplitudes for reflections h,k,l and -h,-k,-l are generated and output as separate reflections. In this case, the column ISYM may also be assigned if it is present: this is a flag from Truncate which = 0 if F comes from from both positive (hkl) and negative (-h-k-l) Bijvoet reflections, = 1 if only from F+ and = 2 if only F-

MAIN

This gives output suitable for the MAIN program. The output file contains H K L FP SIGFP and optionally PHIB and FOM if they are specified on the LABIN line. Alternatively, if FC is specified on the LABIN line, then FP and FC are interpreted as the real and imaginary parts respectively of a calculated F, and output as a "COMPLEX" field.

SCAL

This gives pseudo-SCALEPACK output which is needed as input to the SOLVE package. The output file assigned to HKLOUT is ASCII and writes out H K L I(+) SIGI(+) I(-) SIGI(-), with the format (3I4,4F8.1). The output may need to be rescaled to fit this format.

USER <format>

The output file is of the form H K L ? ? ... where the user can specify which columns are to be output, how many and in what format. Ten dummy labels (DUM??) are available to assign to any column and are output as real. Also, there are ten dummy columns (IDUM??) which are output as integer. The order of the data in the ASCII file are taken from the order of the program labels specified on the LABIN card e.g. LABIN FP=FP1 DP=DP1 SIGFP=SIG1 SIGDP=SIGDP1 would give the order H K L FP1 DP1 SIG1 SIGDP1 in the output file. The format must either be of a FORTRAN type with initially three integer items and the rest must be complementary with the LABIN card e.g.

  LABIN FP=FP DUM1=X IDUM1=Y
  OUTPUT USER '(3I4,2F7.1,I4)'

or

  OUTPUT USER *

to use free formatted output. However, all columns after H, K and L will be treated as real numbers.

LABIN <program label>=<file label>

        H, K, L           Indices
        FP, SIGFP         F and Sigma for native
        FPH, SIGFPH       F and Sigma for derivative
        FC, PHIC          F and Phase from model
        FPART, PHIPART    F and Phase from partial structure
        DP, SIGDP         Anomalous difference and Sigma
        I, SIGI           I and Sigma
        F(+), SIGF(+)     F+ and Sigma(F+) 
        F(-), SIGF(-)     F- and Sigma(F-)  used for anomalous output
        I(+), SIGI(+)     I+ and Sigma(I+) 
        I(-), SIGI(-)     I- and Sigma(I-) 
        FPART_BULK_S, PHIPART_BULK_S
                          Partial F and Phase for bulk solvent correction
        W, FOM            Weights
        PHIB              Best phase (experimental)
        HLA,HLB,HLC,HLD   Hendrickson-Lattman coefficients
        FREE              FreeR flag
        ISYM              (see TRUNCATE)
        DUM??             Dummy labels (output as real)
        IDUM??            Dummy labels (output as integer)

Note: when using the DUM?? and IDUM?? labels, the program may generate warnings about column type mismatches. This may happen for instance if an anomalous difference (column type D) is assigned to one of the DUM labels (which is nominally of type R, i.e. 'any other real'). These warnings should be ignored, and the output is not affected.

END

FSQUARED

MONITOR <Nmon>

RESOLUTION <resmin> <resmax>

SCALE <scale>

INCLUDE <keyword> <value> ...

FREER <num>

Include only reflections with FreeRflag = <num>. This is different from the FREEVAL keyword which specifies the freeR set. This will only be applicable if you have assigned the FREE column.

EXCLUDE <keyword> <value> ...

SIGP <Nsig1>, SIGH <Nsig2>

Reflections are excluded if: FP<(<Nsig1>*SIGFP), FPH(<Nsig2>*SIGFPH). Formerly MULTAN reflections were flagged and others unaffected but now not output to any format.

DIFF <difference_limit>

Reflections are excluded if |FP-FPH| (or |DP|) > <difference_limit>

FPMAX <maximum>

Give <maximum> value for FP.

FPHMAX <maximum>

Give <maximum> value for FPH

FREER <num>

Omit reflections with FreeRflag = <num>. This is different from the FREEVAL keyword which specifies the freeR set. This will only be applicable if you have assigned the FREE column.

FREEVAL <num>

MISS <valm>

Also, if MISS is present then when producing isomorphous data, i.e. |FPH-FP|, if either FPH or FP is a MNF then the difference is set to zero and the sigma is twice the measured sigma. For example; FP=MNF SIGFP=MNF, FPH=100 SIGFPH=10 then FPH-FP = 0 and SIG=20.

Notes on INPUT and OUTPUT

subkw = USER

accepts all input columns. Remember the format must match up with the column assigments i.e. assigments to IDUM must be output as integers, all others are treated as real. Warnings about mismatched column types when using DUM or IDUM labels can be ignored; see LABIN keyword.

subkw = XPLOR [or CNS]

accepts all input columns except DUM1 to DUM10 and IDUM1 to IDUM10 and I+, SIGI+, I- and SIGI-.

subkw = SHELX

accepts columns H to SIGFPH and FREE, (DP SIGDP without FP).

subkw = MULTAN

is like SHELX but will only use FREE to include or exclude reflections.

subkw = TNT

is like SHELX except for the use of FREE: if the INCLUDE FREER or EXCLUDE FREER keywords are specified then FREE is used to include or exclude reflections, otherwise the FREE column (if assigned) is output.

subkw = MAIN

accepts H, K, L, FP, SIGFP, PHIB, FOM, FC

subkw = CIF

only H, K, L, FP, SIGFP, DP, SIGDP, FC, PHIC, PHIB, FOM, I+, SIGI+, I-, SIGI-, FPART_BULK_S, PHIPART_BULK_S and FREE are accepted.

You may still have trouble getting exactly the output you want. You can use the unix utilities cut(1) or sed(1) to manipulate the mtz2various output.

Notes on CIF

If the RESO keyword is specified then reflections at higher or lower resolution than the limits given, will be written with _refln.status 'h' or 'l' respectively. The limits will be written to the CIF as the values of _refine.ls_d_res_high and _refine.ls_d_res_low .

If EXCLUDE SIG is given then reflections for which F < <value>*sigma(F), and which satisfy the resolution limits (if given), will be written with _refln.status '<'. The value of _reflns.number_obs excludes all reflections which do not satisfy the condition on sigma(F). All other sub-keywords of EXCLUDE are ignored for CIF output.
N.B. The translation of the RESOLUTION and EXCLUDE SIGP conditions to _refln.status values does not imply that the the use of these conditions is good crystallographic practice. Be prepared to justify why you have excluded any data from your final refinement!

If DP is assigned, anomalous mode is selected, and reflections for which DP has been measured are written out as (hkl)/(-h-k-l) pairs. In this case, if intensities are available, then both I+ and I- must be assigned, or a warning will be printed, and the output CIF will not contain intensities.

Below is a list of the items output to the CIF file:

 _entry.id

 _audit.revision_id
 _audit.creation_date
 _audit.creation_method
 _audit.update_record

 _cell.entry_id
 _cell.length_a
 _cell.length_b
 _cell.length_c
 _cell.angle_alpha
 _cell.angle_beta
 _cell.angle_gamma

 _symmetry.entry_id
 _symmetry.Int_Tables_number
 _symmetry.space_group_name_H-M
 _symmetry_equiv.id
 _symmetry_equiv.pos_as_xyz

 _reflns.entry_id    
 _reflns.d_resolution_high   
 _reflns.d_resolution_low  
 _reflns.limit_h_max     
 _reflns.limit_h_min     
 _reflns.limit_k_max     
 _reflns.limit_k_min     
 _reflns.limit_l_max     
 _reflns.limit_l_min     
 _reflns.number_all     
 _reflns.number_obs     

 _diffrn_radiation_wavelength.id 
 _exptl_crystal.id 
 _reflns_scale.group_code 

These items are the ones per reflection.

 _refln.wavelength_id     Always written
 _refln.crystal_id        Always written
 _refln.scale_group_code  Always written
 _refln.index_h           Always written
 _refln.index_k           Always written
 _refln.index_l           Always written
 _refln.status            Always written
 _refln.F_meas_au         FP
 _refln.F_meas_sigma_au   SIGFP
 _refln.F_calc            FC
 _refln.phase_calc        PHIC
 _refln.phase_meas        PHIB
 _refln.fom               FOM
 _refln.intensity_meas    I+
 _refln.intensity_sigma   SIGI+
 _refln.ebi_F_xplor_bulk_solvent_calc        FPART_BULK_S
 _refln.ebi_phase_xplor_bulk_solvent_calc'   PHIPART_BULK_S

EXAMPLES

    mtz2various HKLIN nicona HKLOUT dell.hkl << EOF
    RESOLUTION 10000 2
    OUTPUT XPLOR
    EXCLUDE SIGP 0.01   # to exclude unmeasured refl.
    LABIN FP=F SIGFP=SIGF FREE=FreeR_flag
    END
    EOF

    mtz2various HKLOUT $CCP4_SCR/toxd.hkl hklin $CEXAM/toxd/toxd <<EOF
    LABIN  FP=FTOXD3 SIGFP=SIGFTOXD3 
    OUTPUT SHELX
    RESOLUTION 100 4
    END
    EOF

• mtz2various.exam

• mtz2various.exam

SEE ALSO

AUTHOR