Jiffies - Revision history

Kay at 13:47, 3 July 2019

2019-07-03T13:47:32Z

← Older revision		Revision as of 15:47, 3 July 2019
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	Here is a one-liner for your .cshrc :		Here is a one-liner for your .cshrc :

	alias scalefactors ~~"egrep ' ..... 0 ...... ........ .. ..... .... ... ...... ......' INTEGRATE.LP"~~		alias scalefactors "egrep '^ ..... ..[0-9] ...... ........ .... ...... ....... ..... ........ ........' INTEGRATE.LP"

	~~This used to work until XDS Version June-2015. Since then it should be~~

	~~alias scalefactors3~~ "egrep '^ ..... ..[0-9] ...... ........ .... ...... ....... ..... ........ ........' INTEGRATE.LP"

	In sh/bash/ksh/zsh syntax the latter would be:		In sh/bash/ksh/zsh syntax the latter would be:

	alias ~~scalefactors3~~="egrep '^ ..... ..[0-9] ...... ........ .... ...... ....... ..... ........ ........' INTEGRATE.LP"		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?)

Docandreas at 07:42, 28 April 2017

2017-04-28T07:42:49Z

← Older revision		Revision as of 09:42, 28 April 2017
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	scalefactors > frames.scales		scalefactors > frames.scales
	and to plot the scale factors, mosaicity and beam divergence of each frame in gnuplot.		and to plot the scale factors, mosaicity and beam divergence of each frame in gnuplot.
	* 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)".

	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)".

	----		----

Docandreas at 07:42, 28 April 2017

2017-04-28T07:42:00Z

← Older revision		Revision as of 09:42, 28 April 2017
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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~~ mosaicity and beam divergence of each frame in gnuplot.		and to plot the scale factors, mosaicity and beam divergence of each frame in gnuplot.
			* 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)".

	This can be done by		This can be done by

Kay: update

2015-09-25T09:39:48Z

update

← Older revision		Revision as of 11:39, 25 September 2015
Line 3:		Line 3:
	alias scalefactors "egrep ' ..... 0 ...... ........ .. ..... .... ... ...... ......' INTEGRATE.LP"		alias scalefactors "egrep ' ..... 0 ...... ........ .. ..... .... ... ...... ......' INTEGRATE.LP"

	~~In sh/bash/ksh/zsh syntax this would~~ be:		This used to work until XDS Version June-2015. Since then it should be

			alias scalefactors3 "egrep '^ ..... ..[0-9] ...... ........ .... ...... ....... ..... ........ ........' INTEGRATE.LP"

	alias ~~scalefactors~~='~~egrep "~~ ..... 0 ...... ........ .. ..... .... ... ...... ......" INTEGRATE.LP'		In sh/bash/ksh/zsh syntax the latter would be:

			alias scalefactors3="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?)

Kay: get rid of sortlattices alias

2009-06-25T15:26:46Z

get rid of sortlattices alias

@@ Line 1: / Line 1: @@
-Here are two one-liners for your .cshrc (FIXME: or should these lines go into .login or .profile?) :
+Here is a one-liner for your .cshrc :
   alias scalefactors "egrep ' .....   0 ...... ........   ..  .....    ....   ...  ......  ......' INTEGRATE.LP"
 In sh/bash/ksh/zsh syntax this would be:
   alias scalefactors='egrep " .....   0 ...... ........   ..  .....    ....   ...  ......  ......" INTEGRATE.LP'
-which could go into ~/.bashrc or something similar. There are many possibilities - best thing might be to search for the file that already contains alias commands:
+which could go into ~/.bashrc (or should it go into .login or .profile?)
 ----

Kay: adjust scalefactors alias to latest XDS version

2009-06-25T15:17:59Z

adjust scalefactors alias to latest XDS version

← Older revision		Revision as of 17:17, 25 June 2009
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	alias sortlattices "egrep '^ .. [aomhtc]' IDXREF.LP \| sort -k3n \| head -12"		alias sortlattices "egrep '^ .. [aomhtc]' IDXREF.LP \| sort -k3n \| head -12"
	alias scalefactors "egrep ' .... 0 ...... ....... .. ..... .... ... ...... ......' INTEGRATE.LP"		alias scalefactors "egrep ' ..... 0 ...... ........ .. ..... .... ... ...... ......' INTEGRATE.LP"

	In sh/bash/ksh/zsh syntax this would be:		In sh/bash/ksh/zsh syntax this would be:

	alias sortlattices='egrep "^ .. [aomhtc]" IDXREF.LP \| sort -k3n \| head -12'		alias sortlattices='egrep "^ .. [aomhtc]" IDXREF.LP \| sort -k3n \| head -12'
	alias scalefactors='egrep " .... 0 ...... ....... .. ..... .... ... ...... ......" INTEGRATE.LP'		alias scalefactors='egrep " ..... 0 ...... ........ .. ..... .... ... ...... ......" INTEGRATE.LP'

	which could go into ~/.bashrc or something similar. There are many possibilities - best thing might be to search for the file that already contains alias commands:		which could go into ~/.bashrc or something similar. There are many possibilities - best thing might be to search for the file that already contains alias commands:

Kay at 14:50, 14 March 2008

2008-03-14T14:50:43Z

← Older revision		Revision as of 16:50, 14 March 2008
Line 59:		Line 59:

	If you simply want the plots and glue them into your lab book, just run (assuming "ms688_2" is the name of your dataset!):		If you simply want the plots and glue them into your lab book, just run (assuming "ms688_2" is the name of your dataset!):
			#!/bin/csh -f
	setenv DATASET ms688_2		setenv DATASET ms688_2

Kay: formatting

2007-11-22T13:20:02Z

formatting

← Older revision		Revision as of 15:20, 22 November 2007
Line 21:		Line 21:

	Example:		Example:
	dikay@turn29:-data/temp% sortlattices		dikay@turn29:-data/temp% sortlattices
	44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0		44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0
	31 aP 0.3 145.8 164.1 245.4 89.9 90.0 89.9 1 0 0 0 0 1 0 0 0 0 1 0		31 aP 0.3 145.8 164.1 245.4 89.9 90.0 89.9 1 0 0 0 0 1 0 0 0 0 1 0

ClemensVonrhein at 12:51, 22 November 2007

2007-11-22T12:51:36Z

← Older revision		Revision as of 14:51, 22 November 2007
Line 4:		Line 4:
	alias scalefactors "egrep ' .... 0 ...... ....... .. ..... .... ... ...... ......' INTEGRATE.LP"		alias scalefactors "egrep ' .... 0 ...... ....... .. ..... .... ... ...... ......' INTEGRATE.LP"

	~~FIXME~~: ~~what~~ are ~~these lines in bash syntax?~~		In sh/bash/ksh/zsh syntax this would be:

			alias sortlattices='egrep "^ .. [aomhtc]" IDXREF.LP \| sort -k3n \| head -12'
			alias scalefactors='egrep " .... 0 ...... ....... .. ..... .... ... ...... ......" INTEGRATE.LP'

			which could go into ~/.bashrc or something similar. There are many possibilities - best thing might be to search for the file that already contains alias commands:

			grep -l "alias " ~/.[a-z]*

	----		----

Kay at 15:42, 15 November 2007

2007-11-15T15:42:22Z

← Older revision		Revision as of 17:42, 15 November 2007
Line 53:		Line 53:
	If you simply want the plots and glue them into your lab book, just run (assuming "ms688_2" is the name of your dataset!):		If you simply want the plots and glue them into your lab book, just run (assuming "ms688_2" is the name of your dataset!):
	setenv DATASET ms688_2		setenv DATASET ms688_2

	scalefactors > $DATASET.scales		scalefactors > $DATASET.scales
	ln -s $DATASET.scales $DATASET.mosaicity		ln -s $DATASET.scales $DATASET.mosaicity