Scaling with SCALA (or better: aimless): Difference between revisions

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Scaling with SCALA (or better: aimless) (view source)

Revision as of 22:54, 14 December 2015

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  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:
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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:


  #!/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
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  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. the usual way)
Kay
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