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Scaling with SCALA (or better: aimless): Difference between revisions
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Scaling with SCALA (or better: aimless) (view source)
Revision as of 11:38, 26 April 2012
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== How to switch off scaling in CORRECT == | |||
If one wants to completely switch scaling off in CORRECT, use | |||
MINIMUM_I/SIGMA=50 | |||
CORRECTIONS= | |||
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: | |||
CORRECTIONS= MODULATION | |||
This can also be combined with NBATCH=1. | |||
== Using pointless and aimless == | |||
[[pointless]] produces a multi-record MTZ file (suitable for SCALA/aimless and TRUNCATE) from XDS_ASCII.HKL, or the XSCALE reflection output file (see also "[ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/runningpointlessandscala.pdf Running Pointless and Scala]"). Note that this may use [[XDS]] for some or most of the scaling. | |||
(see above for how to switch off scaling in [[XDS.INP]], partly or fully). | |||
pointless -copy xdsin XDS_ASCII.HKL hklout XDS_ASCII.mtz | |||
aimless hklin XDS_ASCII.mtz hklout junk_scaled.mtz | tee aimless.log | |||
Obviously, the aimless run can be modified using suitable options. | |||
See below for how to run TRUNCATE. | |||
If one then needs to edit the batch information in this file, the CCP4 program [http://www.ccp4.ac.uk/dist/html/rebatch.html REBATCH] can be used (optional): | |||
rebatch hklin XDS_ASCII.mtz hklout XDS_ASCII_rebatch.mtz <<end_ip | |||
BATCH ALL START 1001 | |||
BATCH ALL PNAME Lysozyme XNAME Hg-Soak DNAME peak | |||
end_ip | |||
sortmtz hklout sortmtz.mtz <<end_ip | |||
H K L M/ISYM BATCH | |||
XDS_ASCII_rebatch.mtz | |||
end_ip | |||
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 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: | 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: | ||
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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 . | ||
[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) | ||