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

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

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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 ==
 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 .
-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.
- 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
-== Using pointless ==
-An alternative way of going from a XDS formatted reflection file to a multi-record MTZ file (suitable for SCALA and TRUNCATE, but not directly for structure solution which requires single-record MTZ files) is via the [[pointless]] program
-(see also "[ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/runningpointlessandscala.pdf Running Pointless and Scala]"). Note that this way also means that [[XDS]] is used to do most of the scaling (because XDS_ASCII.HKL is written by [[CORRECT]]) but this could be switched off in [[XDS.INP]] (partly or fully).
-It's very easy to do:
- pointless -copy xdsin XDS_ASCII.HKL hklout XDS_ASCII.mtz
-The advantage of this route is, that the batch headers of the resulting MTZ file are correct - [http://www.ccp4.ac.uk/dist/html/combat.html COMBAT] doesn't seem to write complete and accurate headers. 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].
 == See also ==
 [[XDSCONV]] to get the MTZ file directly (i.e. circumventing SCALA)