XDSCONV: Output Formats
XDSCONV can produce output files in a format required by
SHELX
selects the output file format 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,Intensity,sigma(I),batch_number.
- h,k,l
- Reflection indices,
- Intensity
- Reflection intensity (could be negative),
- sigma(I)
- Standard deviation of intensity,
- batch_number
- Reflections used for refinement have batch_number=1, while test reflections are marked by batch_number=-1.
CNS
selects the output file format 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). The format of the CNS output file depends on the validity of Friedel's law and whether test-reflections are defined.
If FRIEDEL'S_LAW=TRUE and test-reflections are not inherited nor generated, the CNS-output file generated by XDSCONV looks like
NREFlection=number of reflections (computed by XDSCONV)
ANOMalous=FALSe
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
followed by reflection records for h,k,l,F,sigma(F) in the
FORMAT('INDEx',3I5,' FOBS=',E12.4,' SIGMA=',E12.4)
If FRIEDEL'S_LAW=FALSE and test-reflections are either inherited or generated, the CNS-output file generated by XDSCONV looks like
NREFlection=number of reflections (computed by XDSCONV)
ANOMalous=TRUE
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
followed by reflection records for unique h, k, l and -h,-k,-l (if oberved and not strictly equivalent with h, k, l), written in the
FORMAT('INDEx',3I5,' FOBS=',E12.4,' SIGMA=',E12.4,' TEST=',I2)
The test-flag is set by XDSCONV to 1 for test-reflections and to 0 for reflections in the working set. Also, test-reflections are assumed to have a value 1 when an old CNS-file is used for inheriting the test-set.
CCP4
selects the output file format for the target software package CCP4. The required conversion from intensities to structure factor amplitudes is done by the method of French and Wilson, 1978. The generated output file serves as input file to the CCP4 program f2mtz. In addition, XDSCONV generates the keyworded input file, called F2MTZ.INP, needed to run f2mtz (and cad).
The number and meaning of each item in a reflection record depends on the parameters defined by the user in XDSCONV.INP.
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,Sigma(F),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,Sigma(F) - 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,Sigma(F),DF,Sigma(DF),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,Sigma(F) - Mean structure factor amplitude and its standard
deviation.
DF,Sigma(DF)- Anomalous difference of structure factor amplitudes
and its standard deviation.
For centric reflections where anomalous effects cannot
occur, DF=0 and Sigma(DF)=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 Sigma(DF) are omitted from the
output record.
isym=2: only F- was observed.
F=F-; DF and Sigma(DF) 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.
IALL
selects the output file format 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).
The number and meaning of each item in a reflection record depends on the parameters defined by the user in XDSCONV.INP.
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.
FALL
selects the output file format FALL that provides structure factor amplitudes for 'F+' and 'F-' in addition to their anomalous difference. The conversion from intensities to structure factor amplitudes is done by the method of French and Wilson, 1978. 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 ====> F_NORM (formatted sequential)
Each record consists of one line per reflection, FORMAT(3I5,2ES11.3).
h,k,l,F,Sigma(F)
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,Sigma(F) - Mean structure factor amplitude and its standard
deviation.
------------------------------------------------------------------------
II.) FRIEDEL'S_LAW=FALSE ====> F_ALL (formatted sequential)
Each record consists of one line per reflection, FORMAT(3I5,8ES11.3).
h,k,l,'F+',Sigma('F+'),'F-',Sigma('F-'),F,Sigma(F),DF,Sigma(DF)
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.
F,Sigma(F) - Mean structure factor amplitude and its standard
deviation.
DF,Sigma(DF) - Anomalous difference of structure factor amplitudes
and its standard deviation.
If anomalous effects cannot occur for h,k,l then
DF=0 and Sigma(DF)=0.
Missing data are indicated by Sigma(DF)<0 and the
value of DF indicates which data are missing.
1)Sigma(DF)>0 No missing data
-----------
Anomalous scattering effects are possible and observed for h, k, l.
F = ('Fw+' + 'Fw-')/2 ; Sigma(F) = standard deviation of F
DF = 'F+' - 'F-' ; Sigma(DF)= standard deviation of DF
'Fw+' weighted mean of all reflection amplitudes which are
strictly symmetry related to h, k, l;
'Fw-' weighted mean of all reflection amplitudes which are
strictly symmetry related to -h,-k,-l;
'F+' are the unweighted means of reflections included in the
'F-' estimation of Bijvoet pairs as controlled by the input
parameter DELFRM>0.
2)Sigma(DF)=0 No missing data
-----------
Anomalous scattering effects cannot occur for h, k, l.
F = weighted mean of all reflection amplitudes
which have the same unique indices h,k,l;
Sigma(F) = standard deviation of F
DF = 0 because there is no anomalous scattering effect
Sigma(DF)= 0 standard deviation of DF is theoretically 0.0
3)Sigma(DF)<0 Some data are missing in this record.
----------- The value of DF indicates which data are missing.
a) DF<0: missing data 'Fw+' and DF.
F = 'Fw-' ; Sigma(F) = standard deviation of 'Fw-'
b) DF>0: missing data 'Fw-' and DF.
F = 'Fw+' ; Sigma(F) = standard deviation of 'Fw+'
c) DF=0: missing only data DF. Although both 'Fw+' and 'Fw-'
exist, this case may happen because of the value of
the input parameter DELFRM which controls acceptance
of Bijvoet pairs.
F =('Fw+' + 'Fw-')/2; Sigma(F) = standard deviation of F
Wolfgang Kabsch
page last updated: October 4, 2003
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