Scaling with SCALA (or better: aimless) - Revision history

Kay: /* How to switch off scaling in CORRECT */

2021-11-24T12:41:16Z

How to switch off scaling in CORRECT

← Older revision		Revision as of 14:41, 24 November 2021
Line 5:		Line 5:
	CORRECTIONS=		CORRECTIONS=
	NBATCH=1		NBATCH=1
	in [[XDS.INP]]. MINIMUM_I/SIGMA=50 prevents the sigmas from being adjusted. This also prevents outlier rejection and geometry refinement. Since the latter may be desired it would be most appropriate to use MINIMUM_I/SIGMA=50 only after [[Optimization]] (re-cycling of GXPARM.XDS to XPARM.XDS). Prevention of outlier rejection would be also obtained by using (e.g.) WFAC1=2. NBATCH=1 removes any basic scaling done by CORRECT (as referred to by [~~http~~://journals.iucr.org/d/issues/~~2012~~/05/00/~~tz5002~~/index.html Krojer and von Delft]).		in [[XDS.INP]]. MINIMUM_I/SIGMA=50 prevents the sigmas from being adjusted. This also prevents outlier rejection and geometry refinement. Since the latter may be desired it would be most appropriate to use MINIMUM_I/SIGMA=50 only after [[Optimization]] (re-cycling of GXPARM.XDS to XPARM.XDS). Prevention of outlier rejection would be also obtained by using (e.g.) WFAC1=2. NBATCH=1 removes any basic scaling done by CORRECT (as referred to by [https://journals.iucr.org/s/issues/2011/03/00/xh5026/index.html Krojer and von Delft]).

	A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:		A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:

Kay: /* Using truncate */

2015-12-14T20:54:31Z

Using truncate

← Older revision		Revision as of 22:54, 14 December 2015
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	== Using truncate ==		== Using truncate ==

	~~An example script (contributed by Clemens Vonrhein) to convert XDS_ASCII.HKL into a [http://www.ccp4.ac.uk CCP4] multi-record MTZ file is:~~

	#!/bin/csh -f		#!/bin/csh -f

Kay: Kay moved page Scaling with SCALA to Scaling with SCALA (or better: aimless): more appropriate

2014-06-11T08:47:35Z

Kay moved page Scaling with SCALA to Scaling with SCALA (or better: aimless): more appropriate

← Older revision		Revision as of 10:47, 11 June 2014
(No difference)

Kay: /* See also */

2014-06-11T08:46:29Z

Kay: /* Using combat */

2012-06-23T15:42:06Z

Using combat

← Older revision		Revision as of 17:42, 23 June 2012
Line 38:		Line 38:
	Note: another program to work with those multi-record MTZ files is [http://www.ccp4.ac.uk/dist/html/reindex.html REINDEX].		Note: another program to work with those multi-record MTZ files is [http://www.ccp4.ac.uk/dist/html/reindex.html REINDEX].

	== Using ~~combat~~ ==		== Using truncate ==

	An example script (contributed by Clemens Vonrhein) to convert XDS_ASCII.HKL into a [http://www.ccp4.ac.uk CCP4] multi-record MTZ file is:		An example script (contributed by Clemens Vonrhein) to convert XDS_ASCII.HKL into a [http://www.ccp4.ac.uk CCP4] multi-record MTZ file is:

	#!/bin/csh -f		#!/bin/csh -f
	#
	~~# Scale data from XDS~~
	#
	~~combat hklin XDS_ASCII.HKL hklout junk.mtz << end-combat~~
	~~MONITOR 10000~~
	~~INPUT XDSASCII~~
	~~ADDBATCH 200 # optional: modify batch numbers~~
	~~TITLE Test combat~~
	~~NAME PROJECT myproject CRYSTAL mycrystal DATASET native~~
	~~END~~
	~~end-combat~~

	~~sortmtz hklout junk_sort.mtz << end-sort~~
	~~H K L M/ISYM BATCH I SIGI~~
	~~junk.mtz~~
	~~end-sort~~

	~~scala hklin junk_sort.mtz hklout junk_scaled.mtz << end-scala~~
	~~# scale using default parameters~~
	~~run 1 batch 1 to 1000~~
	~~scales rotation spacing 5 bfactor off~~
	~~# if xds wouldn't have already scaled the data, e.g.~~
	~~# scales rotation spacing 5 secondary 4 bfactor on brotation spacing 20~~
	~~# would be more appropriate (this is what "quickscale" in iMosflm does)~~
	~~anomalous on~~
	~~end-scala~~

	truncate hklin junk_scaled.mtz \		truncate hklin junk_scaled.mtz \
	hklout junk_truncated.mtz <<end-trunc		hklout junk_truncated.mtz <<end-trunc
Line 77:		Line 50:
	end-trunc		end-trunc

	In this way one gets the well-known ~~outputs~~ of ~~[http://www.ccp4.ac.uk/html/scala.html SCALA] and~~ [http://www.ccp4.ac.uk/html/truncate.html TRUNCATE], and the MTZ file junk_truncated.mtz .		In this way one gets the well-known output of [http://www.ccp4.ac.uk/html/truncate.html TRUNCATE], and the MTZ file junk_truncated.mtz .

	~~[http://www.ccp4.ac.uk/dist/html/combat.html COMBAT] doesn't seem to write complete and accurate headers~~.

	== See also ==		== See also ==

	[[XDSCONV]] to get the MTZ file directly (i.e. circumventing SCALA)		[[XDSCONV]] to get the MTZ file directly (i.e. circumventing SCALA)

Kay: /* How to switch off scaling in CORRECT */

2012-06-23T15:39:04Z

How to switch off scaling in CORRECT

← Older revision		Revision as of 17:39, 23 June 2012
Line 5:		Line 5:
	CORRECTIONS=		CORRECTIONS=
	NBATCH=1		NBATCH=1
	in [[XDS.INP]]. MINIMUM_I/SIGMA=50 prevents the sigmas from being adjusted. This also prevents outlier rejection and geometry refinement. Since the latter may be desired it would be most appropriate to use MINIMUM_I/SIGMA=50 only after [[Optimization]] (re-cycling of GXPARM.XDS to XPARM.XDS). Prevention of outlier rejection would be also obtained by using (e.g.) WFAC1=2. NBATCH=1 removes any basic scaling done by CORRECT (as referred to by [http://journals.iucr.org/d/issues/2012/05/00/tz5002/index.html Krojer and ~~van~~ Delft]).		in [[XDS.INP]]. MINIMUM_I/SIGMA=50 prevents the sigmas from being adjusted. This also prevents outlier rejection and geometry refinement. Since the latter may be desired it would be most appropriate to use MINIMUM_I/SIGMA=50 only after [[Optimization]] (re-cycling of GXPARM.XDS to XPARM.XDS). Prevention of outlier rejection would be also obtained by using (e.g.) WFAC1=2. NBATCH=1 removes any basic scaling done by CORRECT (as referred to by [http://journals.iucr.org/d/issues/2012/05/00/tz5002/index.html Krojer and von Delft]).

	A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:		A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:

Kay at 10:38, 26 April 2012

2012-04-26T10:38:50Z

@@ Line 1: / Line 1: @@
 == Using combat ==
 An example script (contributed by Clemens Vonrhein) to convert XDS_ASCII.HKL into a [http://www.ccp4.ac.uk CCP4] multi-record MTZ file is:
@@ Line 41: / Line 79: @@
 In this way one gets the well-known outputs of [http://www.ccp4.ac.uk/html/scala.html SCALA] and [http://www.ccp4.ac.uk/html/truncate.html TRUNCATE], and the MTZ file junk_truncated.mtz .
-If one really wants to completely switch scaling off in CORRECT, one can use
+[http://www.ccp4.ac.uk/dist/html/combat.html COMBAT] doesn't seem to write complete and accurate headers.
 == See also ==
 [[XDSCONV]] to get the MTZ file directly (i.e. circumventing SCALA)

Kay: /* Using combat */

2012-04-26T10:03:51Z

Using combat

← Older revision		Revision as of 12:03, 26 April 2012
Line 44:		Line 44:
	MINIMUM_I/SIGMA=50		MINIMUM_I/SIGMA=50
	CORRECTIONS=		CORRECTIONS=
	in [[XDS.INP]]. MINIMUM_I/SIGMA=50 prevents the sigmas from being adjusted. This also prevents outlier rejection and geometry refinement. Since the latter may be desired it would be most appropriate to use MINIMUM_I/SIGMA=50 only after [[Optimization]] (re-cycling of GXPARM.XDS to XPARM.XDS). Prevention of outlier rejection would be also obtained by using (e.g.) WFAC1=2.		NBATCH=1
			in [[XDS.INP]]. MINIMUM_I/SIGMA=50 prevents the sigmas from being adjusted. This also prevents outlier rejection and geometry refinement. Since the latter may be desired it would be most appropriate to use MINIMUM_I/SIGMA=50 only after [[Optimization]] (re-cycling of GXPARM.XDS to XPARM.XDS). Prevention of outlier rejection would be also obtained by using (e.g.) WFAC1=2. NBATCH=1 removes any basic scaling done by CORRECT (as referred to by [http://journals.iucr.org/d/issues/2012/05/00/tz5002/index.html Krojer and van Delft]).

	A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:		A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:

Kay: /* Using combat */

2011-06-22T08:39:08Z

Using combat

← Older revision		Revision as of 10:39, 22 June 2011
Line 40:		Line 40:

	In this way one gets the well-known outputs of [http://www.ccp4.ac.uk/html/scala.html SCALA] and [http://www.ccp4.ac.uk/html/truncate.html TRUNCATE], and the MTZ file junk_truncated.mtz .		In this way one gets the well-known outputs of [http://www.ccp4.ac.uk/html/scala.html SCALA] and [http://www.ccp4.ac.uk/html/truncate.html TRUNCATE], and the MTZ file junk_truncated.mtz .

			If one really wants to completely switch scaling off in CORRECT, one can use
			MINIMUM_I/SIGMA=50
			CORRECTIONS=
			in [[XDS.INP]]. MINIMUM_I/SIGMA=50 prevents the sigmas from being adjusted. This also prevents outlier rejection and geometry refinement. Since the latter may be desired it would be most appropriate to use MINIMUM_I/SIGMA=50 only after [[Optimization]] (re-cycling of GXPARM.XDS to XPARM.XDS). Prevention of outlier rejection would be also obtained by using (e.g.) WFAC1=2.

			A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:
			CORRECTIONS= MODULATION

	== Using pointless ==		== Using pointless ==

Kay: /* Using combat */

2010-02-19T22:37:16Z

Using combat

← Older revision		Revision as of 00:37, 20 February 2010
Line 26:		Line 26:
	run 1 batch 1 to 1000		run 1 batch 1 to 1000
	scales rotation spacing 5 bfactor off		scales rotation spacing 5 bfactor off
			# if xds wouldn't have already scaled the data, e.g.
			# scales rotation spacing 5 secondary 4 bfactor on brotation spacing 20
			# would be more appropriate (this is what "quickscale" in iMosflm does)
	anomalous on		anomalous on
	end-scala		end-scala
Line 37:		Line 40:

	In this way one gets the well-known outputs of [http://www.ccp4.ac.uk/html/scala.html SCALA] and [http://www.ccp4.ac.uk/html/truncate.html TRUNCATE], and the MTZ file junk_truncated.mtz .		In this way one gets the well-known outputs of [http://www.ccp4.ac.uk/html/scala.html SCALA] and [http://www.ccp4.ac.uk/html/truncate.html TRUNCATE], and the MTZ file junk_truncated.mtz .


	== Using pointless ==		== Using pointless ==

← Older revision		Revision as of 10:46, 11 June 2014
Line 54:		Line 54:
	== See also ==		== See also ==

	[[XDSCONV]] to get the MTZ file directly (i.e. ~~circumventing SCALA~~)		[[XDSCONV]] to get the MTZ file directly (i.e. the usual way)