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(get rid of sortlattices alias) |
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Here is a one-liner for your .cshrc : | Here is a one-liner for your .cshrc : | ||
alias scalefactors "egrep ' ..... | alias scalefactors "egrep '^ ..... ..[0-9] ...... ........ .... ...... ....... ..... ........ ........' INTEGRATE.LP" | ||
In sh/bash/ksh/zsh syntax | In sh/bash/ksh/zsh syntax the latter would be: | ||
alias scalefactors=' | alias scalefactors="egrep '^ ..... ..[0-9] ...... ........ .... ...... ....... ..... ........ ........' INTEGRATE.LP" | ||
which could go into ~/.bashrc (or should it go into .login or .profile?) | which could go into ~/.bashrc (or should it go into .login or .profile?) | ||
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''scalefactors'' finds those lines in INTEGRATE.LP which match a certain pattern of blanks and non-blanks. These are just the lines printed during the INTEGRATE step for each frame. It is very useful (e.g. to find shutter problems, or to "see" the crystal die from radiation damage) to run | ''scalefactors'' finds those lines in INTEGRATE.LP which match a certain pattern of blanks and non-blanks. These are just the lines printed during the INTEGRATE step for each frame. It is very useful (e.g. to find shutter problems, or to "see" the crystal die from radiation damage) to run | ||
scalefactors > frames.scales | scalefactors > frames.scales | ||
and to plot the scale factors | and to plot the scale factors, mosaicity and beam divergence of each frame in gnuplot. | ||
This can be done by | This can be done by | ||
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If you do have bad outliers (e.g. shutter didn't open), and decide that you for now simply want to remove those frames, then you could rename the frames (just append ".bad" to the name), and re-run XDS from the INTEGRATE step. | If you do have bad outliers (e.g. shutter didn't open), and decide that you for now simply want to remove those frames, then you could rename the frames (just append ".bad" to the name), and re-run XDS from the INTEGRATE step. | ||
* Please note that mosaicity is the unrefined mosaicity. The refined mosaicity values for each integrated batch (nine values for different regions on the detector) can be found in the lines containing the string "SIGMAR (degrees)". | |||
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