Difference between revisions of "Xdsconv"

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XDSCONV does outlier rejection in some modes (FIXME: give formula and modes).
 
XDSCONV does outlier rejection in some modes (FIXME: give formula and modes).
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It is good practice to always use FRIEDEL'S_LAW=FALSE - see [[Tips and Tricks]].
  
 
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Revision as of 07:49, 18 March 2008

XDSCONV is the conversion program of the XDS suite.

Possible output formats are SHELX, CNS, CCP4 (for F SIGF DANO SIGDANO), CCP4_F (for F+ F- SIGF+ SIGF-) and CCP4_I (for I+ I- SIGI+ SIGI-).

A typical input file XDSCONV.INP might look like

INPUT_FILE=XDS_ASCII.HKL
INCLUDE_RESOLUTION_RANGE=50 1  ! optional 
OUTPUT_FILE=temp.hkl  CCP4     ! Warning: do _not_ name this file "temp.mtz" !
FRIEDEL'S_LAW=FALSE            ! default is FRIEDEL'S_LAW=TRUE

This produces the file temp.hkl which is then converted to a MTZ file XDS_ASCII.mtz with (these lines are also printed out by XDSCONV):

f2mtz HKLOUT temp.mtz<F2MTZ.INP
cad HKLIN1 temp.mtz HKLOUT XDS_ASCII.mtz<<EOF
LABIN FILE 1 ALL
END
EOF

This latter step is not necessary for CNS and SHELX output formats, which are written directly by XDSCONV. For these output formats, one might use MERGE=FALSE to keep observations separate.


To have control over the column labels, one might want to modify the simple example above as:

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.

In the case of a MTZ file that should be used for molecular replacement and refinement, the CAD step could be used to transfer the R_free flag from a different dataset to this new dataset. Alternatively, change of labels and transfer of columns can be done in the ccp4i GUI.


XDSCONV does outlier rejection in some modes (FIXME: give formula and modes).


It is good practice to always use FRIEDEL'S_LAW=FALSE - see Tips and Tricks.


Hint for long-time XDSCONV users

The latest versions of the program do not require

SPACE_GROUP_NUMBER=
UNIT_CELL_PARAMETERS=

because these are picked up from the header of the input reflection file.