3. Input
3.1 Parameter Files
Program automar continuously saves parameters whenever they change within the program. When starting the program, the saved parameters are read back so the user always finds the latest changes after quitting a automar session. The parameter file read at startup is called automar.mix and resides in directory $MARPRCDATDIR, $AUTOMARDATDIR or $AUTOMARDIR, i.e. mostly in $MARHOME/automar/dat.
If the environment has not been defined, the startup parameter file will be read from the current directory. If the parameter file doesn't exist, program defaults will be used. The program, however, will always create a new parameter file automar.mix.
The parameter file is a keyworded ASCII-file which may be edited, but editing is not recommended, since it is going to be automatically overwritten as soon as parameters within the GUI change.
Parameter files can be saved into user-defined files and can be loaded manually. This is useful when working on a project where you always apply the same set of parameters. The parameter files should carry the extension ".mix" and may be saved using the "File -> Save Parameters ..." menu option. The parameters can be read back by using the "File -> Open Parameters ..." menu option.
There are 2 more special parameter files in $MARPRCDEFDIR with defined file names: automar.defaults and automar.bck. automar.defaults is an editable file which may contain user defaults for all or a set of parameters. It can be loaded directly by choosing menu option Set defaults -> Read automar.defaults. automar.bck is an backup copy of automar.mix that contains the last state of parameters before an automatical update has been done or parameters have been changed manually. It can be loaded by choosing the menu option Set defaults -> Restore last set of parameters.
3.2 Images
automar autodetects image file formats. The program actually looks at contents of files rather than at file names only. automar accepts the following image formats:
Image formats accepted by automar
| Format | Typical suffix | Description |
|---|---|---|
| mar345 | .marXXXX | Images produced by mar345 software, "pck"-compression. |
| marccd | .#### | Images of marCCD detector |
| image | .image | Original format of 180mm/300mm scanners |
| pck | .pck | Images of 180mm/300mm scanners, "pck"-compressed. |
3.3 Spot Files
automar autodetects spot file formats. The program actually looks at contents of files rather than at file names only. automar accepts the following spot file formats:
Spot file formats accepted by automar
| Format | Typical suffix | Description | ||
|---|---|---|---|---|
| MARPEAKS | .pks | Spot search file produced by program marPeaks. | ||
| MARPREDICT | .prd | Spot predictions produced by program marPredict. | ||
| MARPROCESS | .i | MARPROCESS | .i | Integrated spots produced by program marProcess. |
| GENFILE | .gen | Integrated spots produced by program ipmosflm. | ||
| DENZO | .x | Integrated spots produced by program denzo (York format). |
3.4 Others
There is one more special input file in $AUTOMARDIR with a defined file name: cleanup.com. This file is editable and executable. It is executed when choosing the menu option Options -> Tidy up working directory . The script is called from within the program with 2 arguments:
- automar (as identification string)
- working directory
- marProcess: *.prd, *.marPredict *.prf, fort.*
- denzo: hklpredictions, fort.*
- ipmosflm/aimless: ROGUES, SCALES, *PLOT, SPOTOD, COORD*, fort.*
- XDS/XSCALE: *.pck, INTEGRATE.HKL
| File name or extension | Produced by program ... |
|---|---|
| .prd | marPredict, marProcess |
| *.marPredict | marPredict |
| SPOTOD | ipmosflm |
| COORD* | ipmosflm |
| .gen | ipmosflm |
| hklpredictions | denzo |
| fort.* | marProcess, ipmosflm, denzo |
| ROGUES | aimless |
| SCALES | aimless |
| *PLOT | aimless |
| scerror.dat.* | scerror |
| *.pck | XDS |
| INTEGRATE.HKL | XDS |
Appendix 6.2 shows a template for file
cleanup.com.