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

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

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An example script to convert XDS_ASCII.HKL into a [http://www.ccp4.ac.uk CCP4] multi-record MTZ file is:
== How to switch off scaling in CORRECT ==


  #!/bin/csh -f
If one wants to completely switch scaling off in CORRECT, use
  #
  MINIMUM_I/SIGMA=50
  # Scale data from XDS
  CORRECTIONS=
#
  NBATCH=1
combat hklin XDS_ASCII.HKL hklout junk.mtz << end-combat
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]).
MONITOR 10000
 
INPUT XDSASCII
A good option might be to make CORRECT only do MODULATION correction since this is not easily available in SCALA:
ADDBATCH 200            # optional: modify batch numbers
  CORRECTIONS= MODULATION
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
anomalous on
  end-scala
   
   
truncate  hklin  junk_scaled.mtz \
This can also be combined with NBATCH=1.
          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 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 .
== 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).


The equivalent XDSCONV way of obtaining a MTZ file would be just:
  pointless -copy xdsin XDS_ASCII.HKL hklout XDS_ASCII.mtz
  INPUT_FILE=XDS_ASCII.HKL
  aimless hklin XDS_ASCII.mtz hklout junk_scaled.mtz | tee aimless.log
INCLUDE_RESOLUTION_RANGE=50 1  ! optional
OUTPUT_FILE=temp.hkl  CCP4    FRIEDEL'S_LAW=FALSE
(XDSCONV picks up space group and cell parameters from XDS_ASCII.HKL.) After running [[XDSCONV]] one would then run
  f2mtz HKLOUT temp.mtz<F2MTZ.INP
cad HKLIN1 temp.mtz HKLOUT junk_xdsconv.mtz<<EOF
LABIN FILE 1 E1=FP E2=SIGFP E3=DANO E4=SIGDANO
LABOUT FILE 1 E1=FP E2=SIGFP E3=DANO_sulf E4=SIGDANO_sulf
END
EOF


----
Obviously, the aimless run can be modified using suitable options.


Another 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) is via the [http://www.ccp4.ac.uk/prerelease_page.php#pointless pointless] program by [ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/ Phil Evans]:
See below for how to run TRUNCATE.


Scaling and Assessment of Data Quality, Philip Evans, Acta Cryst D 62, 72-82.
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):
 
(see also "[ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/runningpointlessandscala.pdf Running Pointless and Scala]").
 
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
  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
Line 72: Line 37:


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)
Kay
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