ABSURD (CCP4: Supported Program)
NAMEabsurd - for initial processing of intensity files from MADNES
SYNOPSISabsurd madhkl foo_in.mtz hklout foo_out.mtz absin foo.clm plot foo.plt
[Keyworded input] SCALA for scaling/merging, after sorting by SORTMTZ.
The input intensity file(s) may be either the INTFIL output from Madnes itself (eg using Eval 6) (see FILE keyword), or the binary unmerged file from PROCOR (see UFILE keyword): in the latter case, a corresponding Madnes savefile must be read as well.
ABSCOR, ACCEPT, BATCH, BTITLE, CRYSTAL, FILE, LIMITS, NOABSCOR, OBLIQUE, PROCESS (compulsory), REINDEX, REJECT, SCALE, SPLIT, SYMMETRY (compulsory), TITLE, TOOFAR, UFILE
The spherical harmonic coefficients which define the calculated surface, and the observed data are written out to a file filename.CLM. This can be processed into a form which can be viewed with Frodo (see below).
Keywords PLOT & NOPLOT control whether the observed and fitted absorption curves are plotted to a plotfile (logical name PLOT). The default is to plot them. The curves are expressed in the polar angles theta (latitude) and phi (longitude, not to be confused with the Eulerian or diffractometer angles phi), relative to the diffactometer Phi spindle. The observed values are plotted as a solid line (dashed for regions OMITted, see below).The calculated line is drawn dotted.
The keyword OMIT introduces one or more ranges of Phi to be omitted from the fitting. This may be used to exclude regions of the measured curves where the X-ray beam have missed the crystal. The Phi range may either be specified as the Eulerian angle Phi as output by Madnes (default, or keyword EULERIAN preceeding OMIT), or as the polar angle Phi as output by ABSURD (keyword POLAR preceeding OMIT). This second option allows the curve to be processed once, plotted, and a region to omit determined from the plot. In order to fit the curve, the PROCESS keyword must be used, so that the save data is read from the reflection input file. If you are just processing the absorption curve to check the fit, a Save file may be given instead of a reflection data file. Note that the OMIT keyword must follow all other keywords on the line, and is followed by one or more pairs of numbers giving the phi ranges.
Each ABSCOR command will cause the curve to be read & fitted when the next PROCESS command is read. This curve will then be used for all subsequent PROCESS commands until the next ABSCOR or NOABSCOR command.
Read the symmetry operations, specified as the name (eg P212121), the International Tables number, or as a series of SYMMETRY commands giving the symmetry operations (eg SYMMETRY X,Y,Z * -X,Y+1/2,-Z)
This last option is not recommended. The symmetry matrices are read from a standard file (logical name SYMOP), are printed, and are used to reduce the reflections to an asymmetric unit. The column M/ISYM in the output file contains the number of the symmetry operation used to do this, odd numbers correspond to +hkl, even numbers to Bijvoet-related reflections -hkl. The asymmetric unit is selected according to the rule printed out with the symmetry
eg file Madnes_save_file process ufile profit.hkl process
Flag Default Error Number Setting Condition 1 accept Not found (ie weak) 2 accept On YMS edge 3 accept On ZMS edge 4 accept On Phi edge 5 reject Too far from YMS 6 reject Too far from ZMS 7 reject Too far from Phi 8 reject Too big in YMS 9 reject Too big in ZMS 10 reject Too big in Phi 11 reject Background bad 12 reject Background sd bad 13 reject Negative sd 14 accept Fobs <= 0.0 15 reject Bad pixels 16 reject Overflow
[air-absorption] [window-absorption] [window-thickness]
Apply oblique incidence correction to data, to correct for absorption by air and by the black-paper window. This should be done if it has not been included in the non-uniformity correction (from June 1989 Phase1 onwards). If omitted, the parameters default to those for CuKalpha
air-absorption [0.00108] absorption coefficient of air / mm window-absorption [0.552] absorption coefficient of window / mm window-thickness [0.1634] thickness of window (mm)
eg reindex k, h, -l reindex h, -k, -h/2-l/2Cell dimensions will be recalculated for the redefined cell. Be careful that the index transformation preserves the hand of the axes, ie that the matrix has a positive determinant. The program will not allow you to invert the hand (eg k,h,l is forbidden, k,h,-l is allowed). If the transformation leads to fractional indices for some cases (as in the 2nd example above), these reflections will be rejected. If the reindexing operations include translations, then the orientation data in the output file will not be strictly correct. Translations (eg h,k,l+1) can be useful if you have misindexed your crystal by eg 1 lattice point (usually along the spindle axis). However, in this case, you OUGHT to reprocess the data.
Process the currently-defined input file (from FILE command or logical name MADHKL).
The input files are
The output files are
HKLOUT MTZ file output. Each batch has an orientation block as defined in mtzlib.doc for area detectors. The columns for each reflection are H K L indices M/ISYM symmetry number, ie number of the Laue-group matrix used to reduce this reflection to the asymmetric unit BATCH batch number I, SIGI intensity and standard deviation IERROR error flag from Madnes TIME accumulated exposure time in minutes XDET,YDET detector coordinates of reflection (pixels) XDET = Yms, YDET = Zms (ie Mosflm convention) ROT rotation angle (degrees)
This file must be sorted on H K L M/ISYM BATCH before processing by BEAMCOR or SCALA. Several files may be sorted together by SORTMTZ.
ABSIN.CLM if the ABSCOR option is used, file containing spherical harmonic coefficients and observed absorption data. See below for further processing of this file. The file contains:- line 1: LMAX, LORD, NCLM, CUT LMAX = maximum order of spherical harmonics LORD = 2 for centro-symmetric surface (always) NCLM = number of coefficients CUT = standard deviation cutoff for observations line 2,3: NCLM coefficients rest of file: theta, phi, reject-flag, relative observed intensity, observed intensity, calculated intensity
The program takes one line of input, a title for the output map (see example)
absurd hklout junk plot absplot << eof TITLE This is the overall title for the file SYMMETRY 19 CRYSTAL 1 ABSCOR abscurve.dat PLOT POLAR OMIT -70 +20 # # Abscurve.dat is the file written by Madnes>Det>abscol # SCALE 2.5 # # Process three files in succession. The absorption # correction applies to all 3 # (unless there is another ABSCOR command) # FILE mmndump1_001.dat BATCH 41 BTITLE Crystal 1, run 1 # this title is for this batch only PROCESS FILE mmndump1_002.dat BATCH 42 BTITLE Crystal 1, run 2 PROCESS FILE mmndump1_003.dat BATCH 43 BTITLE Crystal 1, run 3 PROCESS eof # # Send plotfile to plotter pltdev absplot.plt # exit A VMS example $ absurd hklout x12_absd plot x12plot TITLE RBP x12 3.3A with absorption correction, Q85C + MeHg ABSCOR x12.ABS SPLIT 4 SYMMETRY I4132 CRYSTAL 12 BTITLE x12 rotated about arbitrary axis, 3.3A BATCH 100 FILE x12_b_001 PROCESS FILE x12_c_001 PROCESS FILE x12_c_002 PROCESS $! $ laserprint /port=laser4port /plot x12plot.plt $! $ sort: sortmtz hklin x12_absd hklout x12_absd_s - H K L M/ISYM BATCH $! $UNDUPL x12_absd_s.mtz x12_absd_su.mtz /lims on dx,dy (mm), phi,chi,omega x12_rej.lis $!
AUTHORMTZ version May 1991 Phil Evans