Table of Contents
marIndex - Fully automatic autoindexing program using diffraction spots
collected by program marPeaks.
marIndex [ -v <mode> ] [ -s <service>
] [ -f FILE ] FILE
marIndex reads a list of reflexion spot
coordinates from one or more images as obtained by program marPeaks. The
spot file produced by marPeaks (<name>.pks) features a header that contains
the most relevant parameters required for autoindexing. These parameters
are wavelength, sample-to-detector distance, approximate beam position,
and goniometer angle(s)/spindle axis setting(s) of the image(s), as well
as the pixel size.
Otherwise, marIndex can read a keyworded parameter file
(<name>.ctrl or <name>.amp; amp="automar parameters") with the keywords described
below. marIndex will also consider the contents of a file called <name>.prm
if it resides in the current directory. This ".prm" file is supposed to contain
fixed parameters valid for all images of a data set, e.g. the wavelength
or distance. Note, that the entries found in the ".ctrl" file will take precedence
over entries found in the ".prm" file! The keyword nomenclature for both
".prm" and ".ctrl/.amp"-files is the same.
marIndex does not need a guess even
for the order of magnitude of the lattice constants; nor is marIndex necessarily
lost if the beam position is off by more than half the spot distance. marIndex
will usually come up with the right answers if at least 20 spots are available;
in favourable cases it may succeed with as few as a dozen.
marIndex produces
a file (<name>.amp) containing all input parameters and - in addition - the
resulting cell axes, angles, orientation and zone axes refinement parameters.
This file can be taken directly as input to prediction (marPredict) and
integration (marProcess). marIndex also produces an extensive log file called
<name>.marIndex.
The program can be run stand-alone but usage within the graphical
user interface automar is highly recommended.
- -h
- Print usage information.
- -v <mode>
- Verbose mode. <mode> can be "p" (for protocol). Gives more extensive
program log output.
- -s <service>
- Gives the type of orientation matrix output
format. Can be "NONE" or any combination of "AUTOMAR", "DENZO", "MOSFLM",
"MARXDS" and "XDS". The default is "NONE" for the standard output (on terminal
window) and "AUTOMAR MOSFLM DENZO XDS" for the log file. When using "-s
MOSFLM", a file called <name>.UMAT will be produced that contains the matrix
in MOSFLM notation (which should be entered then with keyword UMAT) and
a file called <name>.mosflm containing keywords to be used within MOSFLM.
- FILE
- Read diffraction parameters from file FILE, e.g. marIndex.ctrl. Alternatively,
a spot file as produced by marPeaks (<name>.pks).
The coordinate
system is defined such that X is the horizontal axis and Y the vertical
axis, the origin being the lower left corner when seen in direction of
the beam onto the detector surface.
Detector tilt and rotation are defined
by 3 rotation angles around X, Y, and the detector normal Z (axis not
used otherwise), in the math. +ve sense. Positive tilt_X or tilt_Y bring
the upper or left half of the detector closer to the sample. A positive
rotation (turn_Z) rotates the detector plane counter-clockwise as seen from
the sample.
To avoid confusion, crystal coordinates x & y are defined parallel
to X & Y, making the z-axis anti-parallel to the beam direction.
Crystal axes
are defined by permutation indices {l1,l2,l3} with values +|-(1,2,3) where
"1" denotes the a*-axis, "2"=b*, "3"=c*; "+" means parallel and "-" anti-
parallel to a coordinate axis; in this way l1 gives the reciprocal crystal
axis along the x-axis; l2 that one "up" in the x-y-plane. The l3 index (towards
the radiation source) is redundant, but may be forced to yield a left- handed
system.
Orientation angles are given in degrees and are numbered the same
way but are applied from right to left:
- phi_z
- rotates around the z-axis
(counter-clockwise when looking along the beam). Applying this missetting
first allows easy setting of e.g. a crystallographic face diagonal along
the rotation axis by phi_z = 45. + delta_phi_z, where delta_phi3 is the
true missetting angle. The 45 deg. are not altered by any of the other phi_x,phi_y
- phi_y
- rotates around the y-axis, again in the math. +ve sense.
- phi_x
- is
a mere correction of the spindle axis (if it is horizontal) and may thus
be used as an offset for the PHI axis reading.
Example: hexagonal c*-axis
along the (horizontal) PHI-axis, a* up => (3,1,2). phi_x=30 brings the b*-axis
exactly against the beam.
marIndex always produces setting parameters with
missetting angles < 45 deg. (except for trigonal alternatives) and assigns
permutation indices accordingly, although an easier permutation of axes
may exist - especially in the case of equivalent axes (e.g. a cubic crystal
might always be described by "axes 1 2 3" but may be assigned "3 1 2").
The accepted keywords in the parameter file (either ".amp", ".ctrl"
or ".prm) are given below. Lines starting with "!", "#", "*", "----" or "remark"
will be ignored. In addition, a "!" somewhere in a line will make the rest
of the line to be ignored. Keywords are case insensitive.
- SPAC*e-group <number>
or <name>
- Space group of crystal.
Default: SPACE-GROUP ? (undefined)
- LATT*ice <name>
- Bravais lattice or extinction
group: one of "aP", "mP", "mC", "mA", "mB", "mI", "hP", "hR", "oP",
"oC", "oI", "oF", "tP", "tI", "cP", "cI", or "cF". Obsolete when
SPACEgroup given.
Default: LATTICE ? (undefined)
- CELL <a> <b> <c> [<alpha> <beta> <gamma>]
- Unit cell
parameters in Ang, deg. The cell parameters will not really be used by the
program, but if given, a consistency check will be made with the given
spacegroup or lattice.
Default: undefined
- DIST*ance <dist> [tolerance] [fix]
- Sample to detector
distance in mm. Optional arguments are a tolerance (in percent of the input
distance) for shifts of the distance during parameter refinement. A tolerance
value of 0.0 can be given as argument "fix", i.e. the distance will not be
allowed to vary.
Default: DISTANCE 100.0 1.0
- WAVE*length <lambda1> [delta_lambda1/lambda1]
[<lambda2> [delta_lambda2/lambda2]]
- Wavelength of radiation in Ang.. May be
given as "Cu", "Mo" or "Ag". With "Mo" or "Ag" the program will consider
K-alpha_1 and K-alpha_2 components of the radiation. With "Cu", the program
will consider K-alpha and K-beta components of the radiation. Delta_lambda1/lambda1
is optional (e.g. 0.003 for Cu-radiation). A second wavelength and its delta_lambda2/lambda2
may optionally be given.
Default: WAVELENGTH Cu
- MOSA*icity <mosa_x> [<mosa_y>]
- Mosaic spread of crystal
in degrees. When no y-component is given, the mosaicity will be assumed
to be isotropic. The mosaic spread will not actually be used by the program,
but when specified no refinement will be carried out.
Default: undefined
- DIVE*ergence <div_y> [<div_x>]
- Divergence of the beam in
degrees. When no x-component is given, the divergence will be assumed to
be isotropic. The divergence will not actually be used by the program, but
when specified no refinement will be carried out.
Default: undefined
- CHI <chi>
- CHI angle in degrees.
Default: CHI 0.0
- OMEGA <omega>
- OMEGA angle in degrees.
Default: OMEGA 0.0
- TWOTHETA <twotheta>
- 2-Theta angle in degrees.
Default: TWOTHETA 0.0
- RESO*lution <max>
- Max. resolution limit in Angst.
Default: RESOLUTION 2.0
- BEAM*center <xcen> <ycen> [fix]
- Center of beam in x
and y (pixels). By providing the optional argument "fix", the center will
not be refined.
Default: Half plate diameter.
- PIXE*lsize <pixelsize_x> [<pixelsize_y>]
- Pixelsize
in x (and y, if differing from x) in mm .
Default: PIXELSIZE 0.150
- IMAG*e <ffrm> <lfrm> START <phi_beg> OSC <dphi>
- First
(<ffrm>) and last (<lfrm>) image for which to generate reciprocal lattice coordinates,
the PHI position at the beginning of image <ffrm> (<phi_beg>) and the delta-PHI
(<dphi>) per image.
Example: IMAGE 1 1 START 0.0 OSC 1.0
- PEAK*file <peak_file.pks>
- Specifies the
complete spot file name as produced by program marPeaks. This keyword is
mandatory when used on a input file of type ".ctrl" or ".amp" and obsolete
on a peak file as input file.
Example: PEAKFILE ./index.pks
- SCAN <size_x> [<size_y>]
- No. of pixels in image
in 1 dimension. Use one of: 1200, 1600, 1800, 2000, 2300, 3000 or 3450 (all
IP) or 2048 (CCD)
Default: read from peak file header
- AXES <l1 l2 l3>
- Direction of the reciprocal
axes in marIndex notation. When given, the assignment will be forced, leading
to possibly large orientation angles.
Default: undefined
- TILT <tilt_X> [<tilt_Y>]
- Detector tilt in the horizontal
plane and in the vertical plane in degrees.
Default: TILT 0.0 0.0
- ROT <turn_Z>
- Detector rotation with respect to the
projection of the 2-theta axis in degrees.
Default: ROT 0.0
- SKEW <tilt_X> <tilt_Y> <turn_Z>
- Combines keywords TILT and
SKEW (see above).
Default: SKEW 0.0 0.0 0.0
- (BEAM-)STOP <x_beg> <y_beg> <x_end> <y_end> [<width>]
- Reject
spots within a rectangle defined by <x&y_beg> in the lower left corner to
<x&y_end> in the upper right corner (in pixel units). To exclude areas that
are not running parallel to the horizontal and vertical plane, specify
the <width> of the rectangular section. In that case, the x&y-coordinates given
mark the start and end of a line and 2*<width> would be the thickness of
the line .
Default: STOP 0 0 0 0 0
- FIX [beam or center] [distance] [cell]
- Given parameters
will be excluded from refinement.
marIndex requires the input
file to reside in the local directory. Input files can be just a spot file
produced by program marPeaks in "AUTOMAR" format (i.e. extension .pks). Otherwise,
a control parameter file (<name>.ctrl) and/or the output parameter file of
marIndex (<name>.amp) can be used. Parameters will also be read from a file
<name>.prm if it exists in the local directory. Parameters found in this file
will override parameters given in any other input file!
- Log
file <name>.marIndex
The program produces an ASCII log file. The <name> will be taken from the
input file to be used, e.g. if the input file is called marIndex.ctrl, the
<name> will be "marIndex".
- Parameter file: <name>.amp
The program produces an ASCII parameter file with parameters obtained from
autoindexing and zone axes refinement. The keywords are identical to those
of the input control file, so the .amp file can be taken directly as input
for another run of marIndex. Please note, that the first run always writes
a lattice and/or spacegroup into the ".amp" file, so to rerun the program
with the ".amp"-file will always end with the refined cell in the lattice
as suggested by the first run.
Depending on the <service> switch on command
line input, marIndex will produce one or more files with orientation parameters
and/or keyworded parameter files compatible to programs MOSFLM, DENZO
and XDS:
- MOSFLM matrix: <name>.UMAT
Orientation matrix file suitable as argument for keyword UMAT in MOSFLM.
<>.- Keyworded command file for MOSFLM with refined parameters for distance,
beam center, cell, etc.
- DENZO command file: <name>.DENZO
Keyworded command file for DENZO with refined parameters for distance,
beam center, cell, orientation, etc.
- MARXDS command file: <name>.marXDS
Keyworded command file for marXDS with refined parameters for distance,
beam center, cell, orientation, etc.
- XDS matrix: XPARM.XDS
Orientation matrix file suitable for program XDS and marXDS.
The
program itself is called in a very simple way:
- marIndex marIndex.ctrl
- The
program reads parameters from file marIndex.ctrl in the local directory.
- marIndex xtal_001
- The program reads parameters from file xtal_001.amp in
the local directory. If xtal_001.amp doesn’t exist, xtal_001.pks will be tried.
- marIndex xtal_001.pks
- The program reads spots from file xtal_001.pks in
the local directory. If xtal_001.pks doesn’t exist, xtal_001.mar will be tried.
Note, that the ".pks" file contains all required parameters (distance, wavelength)
in the file header!
Example of file contents of the input parameter file:
| spacegroup | ? |
| wavelength | 1.54179 |
| distance | 90.00 |
| scanmode | 1200 x 1200 |
| pixelsize | 0.150
0.150 |
| beamcenter | 600.0 600.0 |
| peakfile | index.pks |
automar, marPeaks, marPredict,
marProcess
Klaus Bartels, marXperts GmbH, Norderstedt, Germany
© Copyright 1997-2003 marXperts GmbH, Norderstedt, Germany
|
| marXperts GmbH | Phone: +49 - (40) - 529 884-0 |
| Werkstr. 3 | FAX: +49 - (40) - 529
884-20 |
| D-22844 Norderstedt - GERMANY | info@marXperts.com |
| www.marXperts.com |
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