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:
- To run the peak search step off-line, type:
marPeaks -l AUTOMAR.peaks marPeaks.ctrl - To run the indexing step off-line, type:
marIndex marIndex.ctrl -
To run the integration step off-line, type:
marProcess marProcess.ctrl (or mosflm.com)
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 |