User's Guide

marXperts GmbH
Werkstr.3
D-22844 Norderstedt / Germany
Tel. +49 (40) 529 884 0
www.marxperts.com

6. Appendix

6.1 Analogy of Text Fields and Program Keywords
6.2 Template for cleanup.com

6.1 Analogy of Text Fields and Program Keywords

6.1.1 Peak Search

Page	Text Field	marPeaks Keyword
Setup	Image directory & name	`template <string>`
Setup	2-Theta,Chi & Omega	`angles twotheta <float> angles chi <float> angles omega <float>`
Setup	Wavelength	`wavelength <float>`
Setup	Distance	`distance <float>`
Setup	PHI-Start	`image START <float>`
Setup	Delta-PHI/Image	`image OSC <float>`
Main	First & last image	`image <integer> <integer>`
Peak Search	Expected no. of spots/image	`target <integer>`
Peak Search	Min. sigma threshold	`peak sigma <float>`
Peak Search	Min. no. of pixels in spot	`peak min <integer>`
Peak Search	Min. distance between spots	`reject separation <float>`
Peak Search	Typical spot size	`peak nboxx <int> nboxy <int> pixmin <int> pixmax <int> dxdy <int> size <int>`
Peak Search	Binning in image	`image bin <integer>`
Exclude area	Beamstop	`exclude beamstop <float>`
Exclude circle	Circle	`exclude circle <float> <float> <float>`
Exclude area	Ring	`exclude ring <float> <float>`
Exclude area	Rectangle	`exclude rectangle <float> <float> <float> <float> [<float>]`
Exclude area	Ice ring	`exclude ice 5*<float>`

6.1.2 Index

Page	Text Field	marIndex Keyword
Setup	Working directory	`peakfile <string>`
Setup	Cell axes & angles	`cell 6x <float>`
Setup	Spacegroup	`spacegroup <integer> or <string>`
Setup	Wavelength	`wavelength <float>`
Setup	Distance	`distance <float>`
Setup	Extension	`scan <integer> x <integer>`
Setup	Pixelsize	`pixelsize <float> <float>`
Setup	Beam center	`beamcenter <float> <float>`
Setup	Polarization	`polar <float> or <string>`

Note: Program marPredict uses 2 hidden sets of parameters resulting from indexing: the crystal orientation and the axis definition, both in marIndex notation. These parameters are given in the input parameter file on keywords orientation and axes

Page	Text Field	marPredict Keyword
Setup	Cell axes & angles	`cell 6x <float>`
Setup	Spacegroup	`spacegroup <integer> or <string>`
Setup	Wavelength	`wavelength <float>`
Setup	Distance	`distance <float>`
Setup	Tilt, twist	`tilt <float> <float>`
Setup	Mosaicity	`mosaicity <float>`
Setup	Extension	`scanmode <integer> x <integer>`
Setup	Pixelsize	`pixelsize <float> <float>`
Setup	Beam center	`beamcenter <float> <float>`
Main	Max. resolution	`radius <float> <float>`
Setup	Divergence	`diverg <float> [<float>]`
Setup	Polarization	`polar <float> or <string>`
Exclude area	Beamstop	`exclude beamstop <float>`
Exclude circle	Circle	`exclude shadow <float> <float> <float>`
Exclude area	Ring	`exclude ring <float> <float>`
Exclude area	Rectangle	`exclude shade <float> <float> <float> <float> [<float>]`
Exclude area	Ice ring

6.1.4 Strategy

Note: Program marStrategy uses 2 hidden sets of parameters resulting from indexing: the crystal orientation and the axis definition, both in marIndex notation. These parameters are given in the input parameter file on keywords orientation and axes

Page	Text Field	marStrategy Keyword
Setup	Cell axes & angles	`cell 6x <float>`
Setup	Spacegroup	`spacegroup <integer>`
Setup	Wavelength	`wavelength <float>`
Setup	Distance	`distance <float>`
Setup	Tilt, twist	`tilt <float> <float>`
Setup	Extension	`scanmode <integer> x <integer>`
Setup	Pixelsize	`pixelsize <float> <float>`
Setup	Beam center	`beamcenter <float> <float>`
Main	Max. resolution	`resolution <float> <float>`
Strategy	Starting PHI	`phi start <float>`
Strategy	Total PHI	`phi total <float>`
Strategy	Delta-PHI per bin	`phi oscillation <float>`

6.1.5 Integrate

6.1.5.1 marProcess

Program marProcess uses the same keywords as program marPredict with a couple of extensions:

Page	Text Field	marProcess Keyword
Setup	First and last image Starting PHI Delta- PHI	`image <integer> <integer> START <float> OSC <float>`
Integrate	Fix/Refine parameters	`fix <string>`
Integrate	Print output	`list <integer>`

6.1.5.2 ipmosflm

Page	Text Field	MOSFLM Keyword
Main	Max. resolution	`resolution <float>`
Main	First & last image	`hklout root_<integer>:<integer>.mtz`
		`process <integer> to <integer>`
Setup	PHI start	`process N1 to N2 start <float>`
Setup	Delta-PHI/image	`process N1 to N2 angle <float>`
Integrate	# of images for 1 profile	`process N1 to N2 block <integer>`
Setup	Image directory & name	`template <string>`
Setup	Extension	`extension <string>`
Setup	Cell axes & angles	`cell 6x <float>`
Setup	Spacegroup	`symmetry <integer>`
Setup	Wavelength	`wavelength <float>`
Setup	Distance	`distance <float>`
Setup	2-Theta	`twotheta <float>`
Setup	Mosaicity	`mosaicity <float>`
Setup	Divergence	`divergence <float> <float>`
Setup	Polarization	`polarization <float>`
Setup	Pixelsize	`pixelsize <float>`
Setup	Beam center	`beamcenter <float> <float>`
Setup	Radial & tang. offset	`distortion roff <float> toff <float>`
Setup	Tilt, twist	`distortion tilt <float> twist <float>`
Setup	Turn	`distortion ccom <float>`

Page	Text Field	MOSFLM Keyword
Integrate	Refine Center (deselected)	`refine fix xcen ycen`
Integrate	Refine Distance (deselected)	`refine fix distance`
Integrate	Refine Tilt (deselected)	`refine fix tilt`
Integrate	Refine Twist (deselected)	`refine fix twist`
Integrate	Refine Roff (deselected)	`refine fix roff`
Integrate	Min. # of reflections	`refine nref <integer>`
Integrate	Max. radius	`refine limit <float>`

Page	Text Field	MOSFLM Keyword
Integrate	Refine Cell (deselected)	`postref fix all`
Integrate	Refine Misset (deselected)	`postref fixed`
Integrate	Use refined div. selected	`postref usebeam`
Integrate	Isotropic div. selected	`postref beam 1`
Integrate	Hor.+vert. div. selected	`postref beam 2`
Integrate	Iso. and hor./vert. div. deselected	`postref beam 0`
Integrate	Min. # of reflections	`postref nref <integer>`
Integrate	Max. angular residual	`postref maxresid <float>`
Integrate	Max. misset shift	`postref maxshift <float>`
Integrate	Use fine PHI slicing	`postref [no]multi`
Integrate	# images for postref.	`postref add <integer>`

Page	Text Field	MOSFLM Keyword
Integrate	# of profiles on detector	`profile xlines <x1 x2 ... > profile ylines <y1 y2 ... >`
Integrate	=> 9	`profile lowres`
Integrate	=> 21	`profile highres`
Integrate	Min. # reflections for profile	`profile nref <N>`
Integrate	Include partials in profile formation (selected)	`profile partials`
Integrate	Optimize measurement box (deselected)	`profile nooptimise`
Integrate	Autodetermine size measurement box (deselected)	`raster <width> <height> <corners> <upper rim> <lower rim>`
Integrate	# of images for 1 profile Autodetermine deselected	`process block <integer>`

Page	Text Field	MOSFLM Keyword
Integrate	Min. spot separation Auto deselected	`separation <float> <float>`
Integrate	Min. spot separation Handle Close selected	`separation close`
Integrate	Detector gain	`gain <float>`

Page	Text Field	MOSFLM Keyword
Exclude area	Beamstop	`backstop radius <float>`
Exclude area	Ring	`resolution exclude <float> <float>`
Exclude area	Rectangle	`limits exclude <float> <float> <float> <float>`
Exclude area	Ice ring	`resolution exclude ice <float> <float>`

6.1.5.3 denzo

Page	Text Field	denzo Keyword
Main	Min./Max. resolution	`resolution limit <float> <float>`
Main	First & last image	`sectopr <integer> to <integer>`
Setup	PHI start	`oscillation start <float>`
Setup	Delta-PHI/image	`oscillation range lt;float>`
Setup	Image directory & template	`raw data file <string>`
Setup	Cell axes & angles	`unit cell <float> <float> ...`
Setup	Spacegroup	`space group <integer>`
Setup	Distance	`distance <float>`
Setup	Wavelength	`wavelength <float>`
Setup	Divergence h/v	`crossfire x <float> y <float>`
Setup	Polarization	`monochromator <string>`
Setup	Missetting angles	`crystal rotx <float> roty <float> rotz <float>`
Setup	Mosaicity	`mosaicity <float>`
Setup	Beam center X	`x beam <float>`
Setup	Beam center Y	`y beam <float>`
Setup	Radial offset	`radial offset <float>`
Setup	Tangential offset	`angular offset <float>`

Page	Text Field	denzo Keyword
Integrate	Box size in x,y	`box <float> <float>`
Integrate	Spot shape in x&y, tilt	`spot elliptical <float> <float> <float>`
Integrate	BKG shape in x&y, tilt	`background elliptical <float> <float> <float>`
Integrate	Profile fit radius	`profile fitting radius <float>`

Page	Text Field	denzo Keyword
Integrate	Sigma threshold	`weak <float>`
Integrate	Refine Cell Distance ...	`fit cell distance ...`
Integrate	# cycles	`go go go ...`

Page	Text Field	denzo Keyword
Exclude area	Beamstop	`ignore circle <float> <float> <float>`
Exclude area	Circle	`ignore circle <float> <float> <float>`
Exclude area	Rectangle	`ignore quadrilateral 8*<float>`
Exclude area	Polygon	`ignore quadrilateral 8*<float>`

Page	Text Field	denzo Keyword
Integrate	Exclude beamstop	`ignore circle <float> <float> <float>`
Integrate	Exclude circle	`ignore circle <float> <float> <float>`
Integrate	Exclude rectangle	`ignore quadrilateral 4*[<float> <float>]`
Integrate	Exclude polygon	`ignore quadrilateral 4*[<float> <float>]`

6.1.5.4 XDS

Page	Text Field	XDS Keyword

6.1.6 Join

When processing data with the mosflm-suite, step Join calls program sortmtz. The only entry for program sortmtz is the reflection file generated by program ipmosflm, named

<string>_<N1>:<N2>.mtz where
<string> is the working directory + image root name, and
<N1> and <N2>are 3-digit integers giving the first and last image processed.

When processing data with programs of the automar-suite, step Join calls program marPost. The following keywords are available for marPost:

Page	Text Field	marPost Keyword
Setup	Image directory & template	`template <string>`
Main	First & last image	`image <integer> <integer>`

6.1.7 Scale

6.1.7.1 marScale

Page	Text Field	marScale Keyword
Setup	Cell axes & angles	`unit cell <float> <float> ...`
Setup	Spacegroup	`space group <integer>`
Setup	Name template	`list <string>`
Scale	No. of resolution shells	`resolution <min> <max> shells <integer>`
Scale	Scale factor on input	`multiplier <float>`
Scale	Reject hkl with I/mean I	`reject <float>`
Scale	Reject hkl with I < sigma	`threshold sigma <float>`
Scale	Output formats	`service <strings>`
Scale	Refine relative B-factor off	`norefine B`
Scale	Anomalous signals on/off	`anomalous \| normal`

6.1.7.2 aimless

Page	Text Field	aimless Keyword
Scale	No. of resolution shells	`bins <integer>`
Scale	No. of refinement cycles	`cycleS <integer>`
Scale	Rotation range per scale	`scales rotation spacing <float>`
Scale	Restrain scale on detector	`tie detector <float>`
Scale	Restrain scale on rotation	`tie rotation <float>`
Scale	Min. sigma threshold for hkl	`exclude sdmin <float>`
Scale	Reject outliers > x*mean	`reject <float>`
Scale	Anomalous signals	`anomalous on/off`
Scale	Sigma correction FULLS	`sdcorr fulL <sdfac> <sdadd>`
Scale	Sigma correction PARTIALS	`sdcorr part <sdfac> <sdadd>`
Scale	Valid partiality range	`partials test <min> <max>`
Scale	Scaling method	`intensities onlyfulls\|partials\| full\|scale_partials`
Scale	Merging method	`final onlyfulls\|partials\| full\|scale_partials`
Scale	Output file contents	`output unmerged original\| unmerged reduced\|average`
Scale	Image range	`run <int> batch <first> to <last>`
Scale	Reference (de/-select)	`run <integer> reference`
Scale	Exclude (images)	`run <integer> exclude <i1 i2 i3 ...>`

6.1.7.3 scalepack

Page	Text Field	scalepack Keyword
Setup	Cell axes & angles	`unit cell <float> <float> ...`
Setup	Spacegroup	`space group <integer>`
Scale	No. of resolution shells	`number of zones <integer>`
Scale	No. of refinement cycles	`postrefine <integer>`
Scale	Restrain scale factor	`scale restrain <float>`
Scale	Restrain B-factor	`B restrain <float>`
Scale	Scale factor for input data	`default scale <float>`
Scale	Scale factor error	`error scale factor <float>`
Scale	Estimated error per shell	`estimated error`
Scale	Rejection level	`write rejection file <float>`
Scale	Rejection probability	`rejection probability <float>`
Scale	Reject hkl	`@reject`
Scale	Anomalous signals	`anomalous`
Scale	Incluse scale.inc	`@scale.inc`
Scale	Output file contents	`[ no merge [original index] ]`
Scale	Image range	`sector <integer> to <integer>`
		`add partials <integer> to <integer>`
Scale	Cell Mosaic Misset	`fit batch cell <integer> to <integer>`
		`fit batch rotx <integer> to <integer>`
		`fit batch roty <integer> to <integer>`
		`fit batch rotz <integer> to <integer>`
		`fit crystal mosaicity <integer> to <integer>`

6.1.7.4 XSCALE

Page	Text Field	XSCALE Keyword

6.1.8 Truncate

Page	Text Field	truncate Keyword
Truncate	Truncate intentesities	`truncate <yes/no>`
Truncate	Use anomalous data	`anomalous <yes/no>`
Truncate	Use low + high res. limit	`rscale <resolmin> <resolmax>`
Truncate	Use explicit number of bins	`ranges <integer>`
Truncate	# of amino acid residues	`nresidues <integer>`
Truncate	Atom names and numbers	`contents <string>`

Note, that keywords nresidues and contents are mutually exclusive, but are compulsory!

6.1.9 Convert

Page	Text Field	mtz2various Keyword
Convert	Output file type	`output shelx\|xplot\|tnt\|cns\|multan\| scalepack`
Convert	Scale factor	`scale <float>`
Convert	Min. sigma threshold	`exclude sigp <float>`

6.2 Template for cleanup.com

The file cleanup.com resides in $AUTOMARDIR and must be editable and executable t is executed when choosing the menu option Options -> Tidy up working directory . The script takes 2 2 arguments.

#!/bin/csh -f
#
if ( $#argv < 2 ) then
	echo "usage: cleanup.com IDENT directory "
	echo "   eg: cleanup.com automar /home/mar/data"
	echo "       IDENT = automar, marFLM, marXDS, marHKL"
	exit
endif
set M = $1
set D = $2
#
cd $D

echo "${M}: Cleaning up directory $D ..."

set A = (`ls *.marPredict *.prd *.prf SCALES ROGUES SPOTOD COORD* *PLOT fort.* hklpred* *PLOT *.pck INTEGRATE.HKL ` )
#
foreach B ( $A )
	/bin/rm -f $B
end