Scaling with SCALA (or better: aimless): Difference between revisions
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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: | 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 == | ||
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]"): | (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]. | ||
== See also == | |||
[[XDSCONV]] to get the MTZ file directly (i.e. circumventing SCALA) | |||
Revision as of 07:51, 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)