PPT Slide

Command-line processing

Most commands in the GUI are available from the command-line; e.g. for the test images, the following could be done:

# detector mar ! not necessary here!

template muldlx1_###.pck

beam 149.79 150.87

autoindex dps image 301

mosaic estimate

go

postref segment 1

process 301 303

go

postref nosegment fix all

process 301 322

go

exit

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Use of the GUI allows the user to check easily how well processing is proceeding; e.g. spot predictions can be compared with the image. However, the speed of processing can be improved greatly if Mosflm is run from the command-line instead. The only procedures unavailable are those associated with visual representation, so if the user is confident about checking the quality of processing by inspection of the log files, this can be a way to improve efficiency.

All the commands can be edited into a command file which the program can then use with the “@command-file” syntax. Note, however, that Mosflm will stop processing from a command file read in this way following the completion of any “PROCESS” command, and wait for further instructions.

Another option is to use the UNIX redirection command with a command file;

[localhost:~/test/muldlx1] harry% ipmosflm < command-file

in this case all the commands in the file will be processed, provided there are no errors.