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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 von 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 | rebatch hklin XDS_ASCII.mtz hklout XDS_ASCII_rebatch.mtz <<end_ip | ||
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BATCH ALL PNAME Lysozyme XNAME Hg-Soak DNAME peak | BATCH ALL PNAME Lysozyme XNAME Hg-Soak DNAME peak | ||
end_ip | end_ip | ||
sortmtz hklout sortmtz.mtz <<end_ip | sortmtz hklout sortmtz.mtz <<end_ip | ||
H K L M/ISYM BATCH | H K L M/ISYM BATCH | ||
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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 truncate == | |||
#!/bin/csh -f | |||
truncate hklin junk_scaled.mtz \ | |||
hklout junk_truncated.mtz <<end-trunc | |||
anomalous yes | |||
nresidue 1049 | |||
labout F=FP SIGF=SIGFP DANO=DANO_sulf SIGDANO=SIGDANO_sulf | |||
end-trunc | |||
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 . | |||
== See also == | |||
[[XDSCONV]] to get the MTZ file directly (i.e. the usual way) |