automar 248x110
Edited on 07-Feb-2017

4. Output

4.1 Parameter Files

As described in section 3.1, the program automar continuously saves parameters whenever they change within the program. The parameter file produced by the program is called automar.mix and resides in directory $MARPRCDATDIR. If the environment has not been defined, the parameter file will be written into the current directory.

Parameter files can be saved into user-defined files by using the the "File -> Save Parameters ..." menu option. The parameter file automatically receives the extension ".mix".


4.2 Command Files

Whenever a program step is run, automar produces an input file for the corresponding program step. The input files are highly standardized so it is very straightforward to find out what has been done during a processing run. Please note, however, that the input files will always be overwritten, i.e. no versions are being kept.

Input files are either executable shell scripts or simple command line arguments for the corresponding program step. Programs can always be run without the user interface by just executing the shell script and/or calling the corresponding program with the corresponding argument.
Examples:

Command files generated by automar

File Description
marPeaks.ctrl Command line argument for program marPeaks.
marIndex.ctrl Command line argument for program marIndex.
marPredict.ctrl Command line argument for program marPredict.
marStrategy.ctrl Command line argument for program marStrategy.
marProcess.ctrl Command line argument for program marProcess.
mosflm.com Shell script for program ipmosflm.
denzo.com Shell script for program denzo.
xds.com Shell script for program XDS.
join.com Shell script for program marPost or sortmtz.
marScale.ctrl Command line argument for program marScale.
aimless.com Shell script for program aimless.
scalepack.com Shell script for program scalepack.
xscale.com Shell script for program XSCALE.
truncate.com Shell script for program truncate.
convert.com Shell script for program mtz2various, mar2mtz, scalepack2mtz, scalepackcvt, etc.

4.3 Log Files

Whenever a program step is run, automar produces a log file for the corresponding program step. The individual programs from the automar-suite (marIndex, marPredict, marProcess, marPost, marScale) produce further output log files.

Log files generated by automar

Step Name of log file
Peak Search AUTOMAR.peaks
Index AUTOMAR.index
index.marIndex = more extensive log file
Predict AUTOMAR.predict
Strategy AUTOMAR.strategy
Integrate AUTOMAR.marProcess
AUTOMAR.mosflm
AUTOMAR.denzo
AUTOMAR.xds
Join AUTOMAR.join
Scale AUTOMAR.marscale
AUTOMAR.aimless
AUTOMAR.scalepack(.*)
AUTOMAR.scerror(.*)
AUTOMAR.xscale
Truncate AUTOMAR.truncate
Convert AUTOMAR.convert

4.4 Other Output Files

Each of the program steps produces specific output files. Most of the resulting files are standardized, so you always know what you will find inside.

Output files generated by processing steps

Step Name Description
Peak Search index.pks Spots used for indexing
Index index.UMAT Orientation matrix for ipmosflm
  index.amp Orientation parameters for marProcess and/or marPredict
Predict marPredict.prd Spot prediction from indexing results
marProcess <root>_###.i Raw integrated intensities
  <root>_###.prd Spot prediction for each image
  <root>_###.marProcess Detailed log files for each image
  <root>_###-###.bgr Image background data for all images
  <root>_###-###.prf Reflection profile data for all images
  <root>_###-###.summary Summary log file for all images
  <root>_###-###.history History of parameter refinement for all images
ipmosflm <root>_###-###.mtz Raw integrated intensities from ipmosflm
  mosflm.gen Spot predictions during integration by ipmosflm
  MOSFLM.summary Summary of data integration by ipmosflm
denzo <root>_###.x Raw integrated intensities from denzo
XDS INTEGRATE.HKL Raw integrated intensities from XDS
  *.pck Background and correction files from XDS
  *.LP Log files from single program steps from XDS/XSCALE
  XDS_ASCII.HKL Scaled and merged intensities by XDS
marPost marPost.Fsq Combined integrated intensities from marPost
  marPost.marPost Detailed log file from marPost
  sort.mtz Sorted integrated intensities
marScale <root>_###-###.marScale Detailed log file of marScale
  <root>_###-###.mean Scaled and merged intensities by marScale
  <root>_###-###.unmerged Scaled but unmerged intensities by marScale
  <root>_###-###.asu Scaled and merged intensities reduced to asym. unit by marScale
  <root>_###-###.dF Anomalous differences by marScale
aimless scale.mtz Scaled and merged intensities by aimless
  NORMPLOT Normal probability plot in xmgr-format by aimless
  ROGUES Rejected reflections by aimless
  SCALES Scale and temperature factors by aimless
scalepack <root>.hkl Scaled and merged intensities by scalepack
  reject Rejected reflections by scalepack
XSCALE XSCALE_ASCII.HKL Scaled and merged intensities by XSCALE
Truncate truncate.mtz Truncated intensities (F square)
Convert <root>.suffix Several types of output formats