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

From XDSwiki
(Using xdsconv to get the MTZ file directly (i.e. circumventing SCALA))
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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:
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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:
  
 
  #!/bin/csh -f
 
  #!/bin/csh -f
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== Using pointless ==
 
== Using pointless ==
  
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 [[pointless]] program
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A better 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]"):
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(see also "[ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prerelease/runningpointlessandscala.pdf Running Pointless and Scala]"). This way is better (according to PRE), but pointless has only been made available recently (and one needs the latest version of the program). It's very easy to do:
  
 
  pointless -copy xdsin XDS_ASCII.HKL hklout XDS_ASCII.mtz
 
  pointless -copy xdsin XDS_ASCII.HKL hklout XDS_ASCII.mtz
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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 xdsconv to get the MTZ file directly (i.e. circumventing SCALA) ==
 
  
The XDSCONV way of obtaining a MTZ file would be just:
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== See also ==
INPUT_FILE=XDS_ASCII.HKL
 
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 E5=ISYM
 
LABOUT FILE 1 E1=FP E2=SIGFP E3=DANO_sulf E4=SIGDANO_sulf E5=ISYM_sulf
 
END
 
EOF
 
  
ISYM column is important if you want to run SHARP afterwards.
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[[XDSCONV]] to get the MTZ file directly (i.e. circumventing SCALA)

Revision as of 06:51, 6 March 2008

Using combat

An example script (contributed by Clemens Vonrhein) to convert XDS_ASCII.HKL into a CCP4 multi-record MTZ file is:

#!/bin/csh -f
#
# Scale data from XDS
#
combat hklin XDS_ASCII.HKL hklout junk.mtz << end-combat
MONITOR 10000
INPUT XDSASCII
ADDBATCH 200             # optional: modify batch numbers
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 \
          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 SCALA and TRUNCATE, and the MTZ file junk_truncated.mtz .


Using pointless

A better 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 "Running Pointless and Scala"). This way is better (according to PRE), but pointless has only been made available recently (and one needs the latest version of the program). 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 - 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 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.


See also

XDSCONV to get the MTZ file directly (i.e. circumventing SCALA)