The input files must be integrated or profile fitted intensity reflection files created by dtintegrate/dtprofit (e.g. dtprofit.ref) and the corresponding d*trek header file created by these programs (e.g. dtintegrate.head)
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
e.g. reindex k, h, -l
reindex h, -k, -h/2-l/2
Cell 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.
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
Specify the project, crystal and dataset names for the output MTZ file. It is strongly recommended that this information is given. Otherwise, the default project, crystal and dataset names are "unknown", "unknown" and "unknown<ddmmyy>" respectively (where <ddmmyy> is the date, with no spaces).
The project-name specifies a particular structure solution project, the crystal name specifies a physical crystal contributing to that project, and the dataset-name specifies a particular dataset obtained from that crystal. All three should be given.
Process the currently-defined input file (from FILE command or logical name MADHKL).
dtreflnmerge <input-file> <output-file> -text
The reflection file header provides a description of all the fields of the reflection file. The header should something like this otherwise the program may fail to convert correctly.
4 20 1 nH ; miller index nK ; miller index nL ; miller index nBadFlag fIntensity ; profile fitted intensity fSigmaI ; sigma of profile fitted intensity fOtherInt ; integrated intensity fOtherSig ; sigma of integrated intensity fObs_pixel0 ; vertical detector coordinate of reflection (Y) fObs_pixel1 ; horizontal detector coordinate of reflection (Z) fObs_rot_mid ; observed reflection centroid fObs_rot_width fCalc_pixel0 fCalc_pixel1 fCalc_rot_mid fResolution fLPfactor ; Lorentz and polarization correction factor fCorrelation sBatch ; Batch number from integrationThe relevant fields used by MADNES are described briefly. The reflections are listed sequentially in free format.
D*TREK header file
The d*trek header file contains a whole lot of information which allows
you to find out just about anything about your experiment (assuming of
course that you and the beamline software remembered to write the correct
values to the image headers. In principle though, the important information
about the experiment should be correct as it is necessary to correctly
analyse your data and should therefore be available for reading by DTREK2SCALA.
The following is a list of the d*trek header items used by DTREK2SCALA.
If you encounter difficulties in converting your data then checking your
d*trek header file may be a place to start. The d*trek header file
can also be specified using the HFILE command. The file is named
dtintegrate.head by default in both d*trek and in DTREK2SCALA.
CRYSTAL_GONIO_VALUES Datum position on MGONAX
goniostat axes (degrees)
CRYSTAL_UNIT_CELL Cell dimensions (A & degrees)
CRYSTAL_SPACEGROUP space group number
CRYSTAL_ORIENT_VECTORS Axis permutation from d*trek.
CRYSTAL_ORIENT_ANGLES "missetting" angles (degrees)
APS1_GONIO_VALUES(6) Crystal to detector distance (mm)
APS1_GONIO_VALUES(1,2,3) detector tilts: DTAU(2) = theta
detector swing angle (degrees)
SOURCE_ORIENT_ANGLES beam tilt angles (degrees)
CRYSTAL_MOSAICITY reflection width (degrees)
SCAN_WAVELENGTH wavelength (A)
SOURCE_SPECTRAL_DISPERSION dispersion (delta lambda/lambda)
SOURCE_CROSSFIRE synchrotron beam parameters:
gammaH, gammaV, Delcor, ?syn4?
scan axis number (1 -> MGONAX)
SCAN_ROTATION(1,2) start and stop values of psi
(D*trek scan axes - usually Omega) (degrees)
SCAN_ROTATION(3) rotation width of each image (degrees)
SCAN_ROTATION(4) time for each image (seconds)
CRYSTAL_GONIO_NUM_VALUES number of crystal goniostat axes
CRYSTAL_GONIO_VECTORS vectors defining the directions
of the MGONAX goniostat axes,
in the d*trek laboratory frame.
GONVEC(I,J),I=1,3 applies to the J'th axis
SOURCE_VECTORS(1,2,3) idealized main beam vector
(anti-parallel to beam!), in d*trek
laboratory frame (excluding the
tilts parameterized by MU)
SOURCE_VECTORS(1,2,3) main beam vector (anti-parallel
to beam!), in d*trek laboratory frame
(including the tilts parameterized by MU)
APS1_DETECTOR_DIMENSIONS detector limits minimum, maximum Yms, Zms
APS1_GONIO_VECTORS vectors defining detector rotations
APS1_DETECTOR_VECTORS vectors defining detector translations
DTREFINE_RMS_MM rms positional errors from last refinement
DTREFINE_RMS_DEG rms rotational errors from last refinement
APS1_GONIO_VALUES(4,5) detector offsets ccx, ccy
DTP_DTINTEGRATE_OPTIONS(11) number of images per batch used in dtintegrate
New common block for d*trek specific things
SCAXIS scan axis
GONAX(3) names of the MGONAX goniostat axes
DETAX(3) names of the detector rotation angles
COMMENT crystal description
N.B. The d*trek laboratory frame has X along the omega axis (towards
base plate of goniometer), Z antiparallel to the X-ray beam and Y
completing a right-handed system. All rotations are right-handed.
This information is encoded in GONVEC & S0, so these are used to
define the frame.
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 IPR, SIGIPR intensity and standard deviation (in this case same as I, SIGI) IERROR error flag from D*TREK XDET,YDET detector coordinates of reflection (pixels) XDET = Yms, YDET = Zms (ie Mosflm convention) ROT rotation angle (degrees) LP Lorentz and polarisation correction (d*trek only) LPThis file must be sorted on H K L M/ISYM BATCH before processing by SCALA. Several files may be sorted together by SORTMTZ.
############## START EXAMPLE 1 ################## dtrek2scala hklout junk.mtz plot absplot << eof TITLE Data processed with d*trek to 1.8A SYMMETRY 20 CRYSTAL 1 BATCH 1 BTITLE Crystal 1, run 1 # this title is for this batch only FILE dtprofit_1.8A.ref HFILE dtintegrate.head PROCESS eof # sortmtz HKLIN junk.mtz HKLOUT dtrek-data.mtz << EOF-sortmtz # # Sort keys since default keys are H K L # H K L M/ISYM EOF-sortmtz ############## END EXAMPLE 1 ##################2. An example which reads two reflection files dataset1.ref and
############## START EXAMPLE 2 ##################
#!/bin/csh -f
#
set ident = mydata
set title = 'A crystal soaked in lots of alcohol'
set lowres = 30
set highres = 1.8
set resol = "${lowres} ${highres}"
set residues = 203
set spacegroup = P43212
set symmetry = 96
set scr = $HOME/tmp
#
#
dtrek2scala hklout ${ident}.mtz > ${ident}.dtrek2scala.log << EOF
TITLE $title
SYMMETRY $symmetry
CRYSTAL 1
BATCH 1
FILE dataset1.ref
HFILE dataset1.head
BTITLE CHI=0, PHI=0
PROCESS
BATCH 300
FILE dataset2.ref
HFILE dataset2.head
BTITLE CHI=30, PHI=0
PROCESS
EOF
#
sortmtz hklout ${ident}_sort.mtz > ${ident}_sort.log << EOF-sortmtz
H K L M/ISYM BATCH
${ident}.mtz
EOF-sortmtz
############## END EXAMPLE 2 ##################