Difference between revisions of "Scaling with SCALA (or better: aimless)"
Revision as of 08:47, 11 June 2014
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 Krojer and von Delft).
A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:
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 "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 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 REINDEX.
An example script (contributed by Clemens Vonrhein) to convert XDS_ASCII.HKL into a CCP4 multi-record MTZ file is:
#!/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 TRUNCATE, and the MTZ file junk_truncated.mtz .
XDSCONV to get the MTZ file directly (i.e. the usual way)