XDSCONV: Output Formats

XDSCONV can produce output files in the following formats


CCP4

This output file format can be used for the target software package CCP4. Intensities are converted to structure factor amplitudes by the method of French and Wilson, 1978. This file can easily be converted to CCP4's MTZ-format by 'f2mtz' (and 'cad'). To this purpose, XDSCONV generates the keyworded input file, called F2MTZ.INP.

Depending upon the value of the keyword FRIEDEL'S_LAW= one of the two output record formats described below will be chosen by XDSCONV.

  I.) FRIEDEL'S_LAW=TRUE

  Each record consists of one line per reflection, free FORMAT.
  Items are separated by a comma, which also allows to recognize missing data.

		 h,k,l,F,SigF,i

      h,k,l    - unique reflection indices. Reflection intensities
		 related by crystallographic symmetry as well as
		 Friedel pairs are averaged and the mean intensity
		 is converted to F.
      F,SigF   - Mean structure factor amplitude and its standard
		 deviation.
	i      - test flag. i=0: reflection belongs to the working set
			    i=1: reflection belongs to the test set.
		 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
		 test flag i will be absent from all output records.

 II.) FRIEDEL'S_LAW=FALSE

  Each record consists of one line per reflection, free FORMAT.

		 h,k,l,F,SigF,DF,SigDF,isym,i

      h,k,l    - unique reflection indices. Reflection intensities
		 related by strict crystallographic symmetry are
		 averaged and the mean intensity in each parity class
		 is converted to F(+) and F(-), respectively.
      F,SigF   - Mean structure factor amplitude and its standard
		 deviation.
     DF,SigDF  - Anomalous difference of structure factor amplitudes
		 and its standard deviation.
		 For centric reflections where anomalous effects cannot
		 occur, DF=0 and SigDF=0.
      isym     - indicates whether an anomalous difference was observed
		 for the reflection h,k,l.
		 isym=0: both F(+) and F(-) were observed.
			 F=(F(+) + F(-))/2; DF=F(+) - F(-)
		 isym=1: only F(+) was observed.
			 F=F(+); DF and SigDF are omitted from the
			 output record.
		 isym=2: only F(-) was observed.
			 F=F(-); DF and SigDF are omitted from the
			 output record.
	i      - test flag. i=0: reflection belongs to the working set
			    i=1: reflection belongs to the test set.
		 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
		 test flag i will be absent from all output records.

CCP4_F

This output file format can be used for the target software package CCP4. Intensities are converted to structure factor amplitudes by the method of French and Wilson, 1978. This file can easily be converted to CCP4's MTZ-format by 'f2mtz' (and 'cad'). To this purpose, XDSCONV generates the keyworded input file, called F2MTZ.INP.

Depending upon the value of the keyword FRIEDEL'S_LAW= one of the two output record formats described below will be chosen by XDSCONV.

  I.) FRIEDEL'S_LAW=TRUE

  Each record consists of one line per reflection, free FORMAT.
  Items are separated by a comma, which also allows to recognize missing data.

		 h,k,l,F,SigF,i

      h,k,l    - unique reflection indices.
      F,SigF   - Mean structure factor amplitude and its standard
		 deviation. Reflection intensities related to h,k,l by
		 crystallographic symmetry as well as Friedel pairs
		 are averaged and the mean intensity is converted to F.
	i      - test flag. i=0: reflection belongs to the working set
			    i=1: reflection belongs to the test set.
		 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
		 test flag i will be absent from all output records.

 II.) FRIEDEL'S_LAW=FALSE

  Each record consists of one line per reflection, free FORMAT.

		 h,k,l,F,SigF,F(+),SigF(+),F(-),SigF(-),i

      h,k,l    - unique reflection indices.
      F,SigF   - Mean structure factor amplitude and its standard
		 deviation. Reflection intensities related to h,k,l by
		 crystallographic symmetry as well as Friedel pairs
		 are averaged and the mean intensity is converted to F.
  F(+),SigF(+) - Mean structure factor amplitude and its standard
		 deviation estimated from the weighted mean of
		 reflection intensities strictly related to h,k,l.
  F(-),SigF(-) - Mean structure factor amplitude and its standard
		 deviation estimated from the weighted mean of
		 reflection intensities strictly related to -h,-k,-l.
	i      - test flag. i=0: reflection belongs to the working set
			    i=1: reflection belongs to the test set.
		 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
		 test flag i will be absent from all output records.

CCP4_I

This output file format can be used for the target software package CCP4. However, no conversion from intensities to structure factor amplitudes is carried out. The purpose of this option is to provide a reflection output file that can easily be converted to CCP4's MTZ-format by 'f2mtz (and cad)' for subsequent analysis by 'truncate'. In addition, XDSCONV generates the keyworded input file, called F2MTZ.INP, needed to run f2mtz (and cad).

Depending upon the value of the keyword FRIEDEL'S_LAW= one of the two output record formats described below will be chosen by XDSCONV.

  I.) FRIEDEL'S_LAW=TRUE

  Each record consists of one line per reflection, free FORMAT.
  Items are separated by a comma, which also allows to recognize missing data.

		 h,k,l,IMEAN,SIGIMEAN,i

      h,k,l    - unique reflection indices.
      IMEAN,   - Mean intensity and its standard deviation of all
     SIGIMEAN    reflections related by symmetry to h,k,l and their
		 Friedel pairs.
	i      - test flag. i=0: reflection belongs to the working set
			    i=1: reflection belongs to the test set.
		 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
		 test flag i will be absent from all output records.

 II.) FRIEDEL'S_LAW=FALSE

  Each record consists of one line per reflection, free FORMAT.

	     h,k,l,IMEAN,SIGIMEAN,I(+),SIGI(+),I(-),SIGI(-),i

      h,k,l    - unique reflection indices.
      IMEAN,   - Mean intensity and its standard deviation of all
     SIGIMEAN    reflections related by symmetry to h,k,l and their
		 Friedel pairs.
   I(+),SIGI(+)  mean intensity and its standard deviation of all
		 reflections related by symmetry to h,k,l
   I(-),SIGI(-)  mean intensity and its standard deviation of all
		 reflections related by symmetry to -h,-k,-l
	i      - test flag. i=0: reflection belongs to the working set
			    i=1: reflection belongs to the test set.
		 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
		 test flag i will be absent from all output records.

CCP4_I+F

This output file format can be used for the target software package CCP4. It provides mean intensities as well as their structure factor amplitudes derived by the method of French and Wilson, 1978. This reflection output file can easily be converted to CCP4's MTZ-format by 'f2mtz (and cad)' for subsequent analysis by 'truncate'. In addition, XDSCONV generates the keyworded input file, called F2MTZ.INP, needed to run f2mtz (and cad).

Depending upon the value of the keyword FRIEDEL'S_LAW= one of the two output record formats described below will be chosen by XDSCONV.

  I.) FRIEDEL'S_LAW=TRUE

  Each record consists of one line per reflection, free FORMAT.
  Items are separated by a comma, which also allows to recognize missing data.

                 h,k,l,IMEAN,SIGIMEAN,FP,SIGFP,i

      h,k,l    - unique reflection indices.
      IMEAN,   - Mean intensity and its standard deviation of all
     SIGIMEAN    reflections related by symmetry to h,k,l and their
                 Friedel pairs.
    FP,SIGFP   - Mean structure factor amplitude and its standard
                 deviation. Reflection intensities related to h,k,l by
                 crystallographic symmetry as well as Friedel pairs
                 are averaged and the mean intensity is converted to F.
        i      - test flag. i=0: reflection belongs to the working set
                            i=1: reflection belongs to the test set.
                 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
                 test flag i will be absent from all output records.

 II.) FRIEDEL'S_LAW=FALSE

  Each record consists of one line per reflection, free FORMAT.

             h,k,l,IMEAN,SIGIMEAN,I(+),SIGI(+),I(-),SIGI(-),
                   FP,SIGFP,F(+),SIGF(+),F(-),SIGF(-),i

      h,k,l    - unique reflection indices.
      IMEAN,   - Mean intensity and its standard deviation of all
     SIGIMEAN    reflections related by symmetry to h,k,l and their
                 Friedel pairs.
   I(+),SIGI(+)  mean intensity and its standard deviation of all
                 reflections related by symmetry to h,k,l
   I(-),SIGI(-)  mean intensity and its standard deviation of all
                 reflections related by symmetry to -h,-k,-l
    FP,SIGFP   - Mean structure factor amplitude and its standard
                 deviation. Reflection intensities related to h,k,l by
                 crystallographic symmetry as well as Friedel pairs
                 are averaged and the mean intensity is converted to F.
  F(+),SigF(+) - Mean structure factor amplitude and its standard
                 deviation estimated from the weighted mean of
                 reflection intensities strictly related to h,k,l.
  F(-),SigF(-) - Mean structure factor amplitude and its standard
                 deviation estimated from the weighted mean of
        i      - test flag. i=0: reflection belongs to the working set
                            i=1: reflection belongs to the test set.
                 If GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.0, the
                 test flag i will be absent from all output records.

CNS

This format can be used for the target software package CNS. The required conversion from intensities to structure factor amplitudes is done by the method of French and Wilson, 1978. The generated CNS output file consists of a header part followed by a sequence of reflection records (one line per reflection).

   header:

      NREFlection=number of reflections as computed by XDSCONV
      ANOMalous=FALSe
      DECLare NAME=FOBS  DOMAin=RECIprocal TYPE=REAL END
      DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
      DECLare NAME=TEST  DOMAin=RECIprocal TYPE=INTE END

   reflection records:

      INDEx h k l FOBS=F SIGMA=SigF TEST=i

      h,k,l    - reflection indices
	F      - structure factor amplitude
      SigF     - standard deviation of F
	i      - test flag
		 i=0: reflection belongs to the working set
		 i=1: reflection belongs to the test set.

If FRIEDEL'S_LAW=FALSE has been specified in XDSCONV.INP the header of the generated CNS output file would be ANOMalous=TRUE instead of ANOMalous=FALSe. Also, each reflection record with unique indices h, k, l would be followed by a record with unique indices -h,-k,-l (if available and not strictly equivalent to h, k, l).
If test reflections are not inherited nor generated, the declaration line NAME=TEST will be omitted from the header part of the output file and the items TEST=i will be absent from all reflection records.


SHELX

This format can be used for the target software package SHELX. The generated output file consists of one record per reflection, FORMAT(3I4,2F8.2,I4), containing the items

		 h,k,l,I,SigI,batch_number

      h,k,l    - reflection indices
	I      - Reflection intensity (could be negative)
      SigI     - Standard deviation of intensity
  batch_number - test flag
		  0: reflection belongs to the working set
		 -1: reflection belongs to the test set.

© 2008-2016, MPI for Medical Research, Heidelberg Imprint.
Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
page last updated: April 24, 2016