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MTZ2VARIOUS (CCP4: Supported Program)NAMEmtz2various - produces an ascii reflexion file for MULTAN, SHELX, TNT, X-PLOR/CNS, MAIN, CIF or user-defined format. This may contain amplitudes, intensities or differences.SYNOPSISmtz2various hklin foo_in.mtz hklout foo_out[Key-worded input file] DESCRIPTIONThis reads an mtz file (assigned to HKLIN) and produces an ASCII file (assigned to HKLOUT)in a suitable form for MULTAN, SHELX, TNT, X-PLOR/CNS, MAIN or in a user-defined format. For SHELX output all quantities are given as intensities, ie F and delF terms are squared. An mmCIF file can also be produced with all the relevant information taken from the MTZ header.There are many options controlled by the assignments on the LABIN line. The most common requirements are: Generate a list of h k l F or h k l I. If anomalous data is present, hkl and -h-k-l will be output on seperate lines. If only FP, SIGFP or IP, SIGIP are assigned on LABIN, hkl FP SIGFP or hkl IP SIGIP is output. If FP,SIGFP and DP, SIGDP are assigned, then F+ and F- are reconstructed, and 2 reflections,, hkl and -h-k-l, are output (X-PLOR,SHELX and CIF formats only) If F(+),SIGF(+) and F(-),SIGF(-) or I(+),SIGI(+) and I(-),SIGI(-) are assigned, then again 2 reflections are output, hkl and -h-k-l . If FP, SIGFP and FPH, SIGFPH are both assigned, then hkl |FP-FPH| SIG|FP-FPH| is output (not applicable for USER and CIF). This can be useful when solving heavy atom positions via direct methods. If DP, SIGDP are assigned, and FP, SIGFP are NOT assigned, then hkl |DP| SIGDP is output (not applicable for USER and CIF).This also can be used to solve for anomalous scatterers using direct methods. The same result can be obtained by assigning FP to FPH(+) and FPH to FPH(-). Then hkl |F(+) -F(-)| SIG|F(+) -F(-)| is output. There is no guarantee that the reflection count is completely robust. Files sometimes have been slightly corrupted; eg DP not present but F(+) and F(-) there. I have TRIED to make sensible decisions in ambigous cases. When using OUTPUT USER you should get what you want, no tricks. KEYWORDED INPUTThe allowed keywords are:OUTPUT, LABIN, END, FSQUARED, MONITOR, RESOLUTION, SCALE, INCLUDE, EXCLUDE, FREEVAL, MISS Compulsory input keywords are OUTPUT and LABIN.OUTPUT [ MULTAN | SHELX | TNT | CIF | XPLOR | CNS | MAIN | SCAL | USER ]The output types are as follows:
LABIN <program label>=<file label>Input labels accepted are: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)Not all columns are used in the various output formats, see Notes on INPUT and OUTPUT. Also, the contents of the columns which are output may depend on which input columns are assigned by LABIN, see DESCRIPTION above. 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. ENDEnd input.FSQUAREDIf this flag is set, the program expects F and SIGF and will output I and SIGI: I = F*F, SIGI = 2*SIGF*F + SIGF*SIGF. These intensities are not necessarily the same as the measured intensities (pre-TRUNCATE) it is better to use the measured values if you have them.MONITOR <Nmon>followed by an integer <Nmon>. Every <Nmon>-th reflection within the resolution range is monitored (printed out).RESOLUTION <resmin> <resmax>Followed by 2 real numbers, <resmin>, <resmax>. This can be used to restrict the output data to the given resolution range.SCALE <scale>The F and SIGF (or I and SIGI) are multiplied by <scale> before output. This may be necessary if you are outputting F_squared into the fixed SHELX format.INCLUDE <keyword> <value> ...Each secondary keyword is followed by a number setting the appropriate limit for excluding data. Possible keywords are FREER.
EXCLUDE <keyword> <value> ...Each secondary keyword is followed by a number setting the appropriate limit for excluding data. Possible keywords are SIGP, SIGH, DIFF, FPMAX, FPHMAX, FREER. If DP is assigned without FP then the exclusion criterion for DIFF are applied to |DP|.
FREEVAL <num>The reflections with FreeRflag = <num> are treated as the freeR set: the default is 0 if FREE is assigned. This is important if you want to include a free-R test in your XPLOR/CNS or SHELX refinement, or you are using the Pannu-Read version of TNT. The FREE column must be assigned with LABIN.MISS <valm>By default, if any data associated with a reflection are missing, i.e. are represented in HKLIN by a Missing Number Flag (MNF), then that reflection will not appear in the output. However, if the keyword MISS is given then these reflections will be output, but with the MNFs converted to <valm>. The latter need not be given, and defaults to 0.0. The other exclusions are still effective.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 OUTPUTNot all INPUT columns are accepted with a particular OUTPUT format. If one has OUTPUT <subkw> then the allowed input columns are given below (see LABIN and OUTPUT) :
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 CIFAll reflections in the MTZ input file will be output to the CIF file. However, there are ways to flag certain reflections with the data type _refln.status. Observed reflections will be flagged with 'o'. Unobserved reflections, i.e. those flagged as missing, will be flagged as 'x'; these reflections will not be added to _reflns.number_obs. The 'free' reflections will be flagged as 'f'. The keyword FREEVAL can be used to indicate this set. Systematically absent reflections are flagged with '-'.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.
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_SmmCIF (at least at version 0.8) makes no provision for the output of derivative data in the same data block as native data. For more information about what these mmCIF categories are, check out the mmCIF dictionary. EXAMPLESmtz2various 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 EOFA runnable unix example script is in $CEXAM/unix/runnable/ A non-runnable unix example script which demonstrates mtz2various used to output anomalous data is in $CEXAM/unix/non-runnable/ SEE ALSOmtzdump, f2mtz, cut(1), sed(1)AUTHOREleanor Dodson, York University |