automar 248x110
Edited on 07-Feb-2017

6. Appendix


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>

6.1.3 Predict

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