XDSCONV: Input Parameters


All input parameters needed for converting data sets (obtained from processing with xds) to serve as input files for various crystal structure analysis packages are collected in the file named XDSCONV.INP. This file must reside in the current directory where XDSCONV will be invoked. To simplify the task of preparing the input file, a file template (example) for XDSCONV.INP is included in the xds package that can easily be edited according to the actual case.

This chapter explains the meaning of all parameters used by the XDSCONV program. Each parameter name consists of a string of characters without intervening blanks or exclamation marks and includes an equal sign as its last character. The value must follow the parameter name on the same line. The parameter names cannot be abbreviated; they are case sensitive, too. Characters in a line to the right of an exclamation mark are comment.

Input parameters of XDSCONV

SPACE_GROUP_NUMBER=

Space-group number of the crystal. The numbers corresponding to each possible space group are defined in the "INTERNATIONAL TABLES I". All 230 space groups are implemented. From the space group number and the unit cell parameters XDSCONV provides a standard set of symmetry operators.

Example: SPACE_GROUP_NUMBER=77
This specifies the tetragonal space group P42

UNIT_CELL_CONSTANTS=

Unit cell parameters a, b, c (Å) and alpha, beta, gamma (degrees). The cell constants must meet the requirements implicated by the space group. First and second setting of monoclinic crystals must be distinguishable by the cell constants. In case a reindexing transformation is specified, the unit cell parameters refer to the new cell.

Example:
UNIT_CELL_CONSTANTS=125.9 125.9 144.7 90.0 90.0 90.0
SPACE_GROUP_NUMBER=77
This specifies the cell constants of a tetragonal crystal obeying P42 space group symmetry. Note that the a and b axes must have identical length and all angles must be exactly 90 degrees as required by the space group.

INPUT_FILE=

File name, its format, and a resolution window for accepting reflections from the input file. This input file will be converted by XDSCONV and must have been generated by a previous run of the scaling program xscale.

File name
is the full path name for locating the input file. The name is restricted to at most 50 characters with no intervening blanks or exclamation marks.
File format
must be specified by one of the keywords:
XDS_ASCII
this is the only reflection file format now being generated and used within the xds-package. All other formats listed below are outdated since August 2000. They are still accepted by xscale.
ANOMAL
the outdated format refers to files ANOMAL.HKL that were used by the old versions of the xds-package for representing anomalous scattering intensity data. This format is described in the old manual xds.man.
NORMAL, OLDHKL
these outdated formats refers to files NORMAL.HKL that were used by the old versions of the xds-package for representing unique intensities in the absence of anomalous scattering effects. OLDHKL and NORMAL are identical formats that are described in the old manual xds.man.
UNIQUE
the outdated format refers to files UNIQUE.HKL that were used by the old versions of the xds-package before November 1998. This format is described in the old manual xds.man.
Resolution window
for accepting reflections from this file consists of: low resolution limit, high resolution limit (Å)

Example
INPUT_FILE=../XSCALE.HKL XDS_ASCII 50 1.2
This specifies an input file, named ../XSCALE.HKL. The file type is XDS_ASCII and the subset of reflections within the resolution range 50 ... 1.2 Å will be accepted by XDSCONV.

OUTPUT_FILE=
FRIEDEL'S_LAW=
MERGE=

File name, target software package, and data type of the output file being generated by XDSCONV.

file name
name assigned to the output file. Should not exceed 50 characters in length. Intervening blanks or exclamation marks are not allowed.
target software package
can be: CNS SHELX CCP4 IALL FALL XtalView
data type of the output file
depends on the parameters FRIEDEL'S_LAW= and MERGE=.
FRIEDEL'S_LAW=TRUE if reflections h, k, l and -h,-k,-l have the same intensities.
FRIEDEL'S_LAW=FALSE if reflections h, k, l and -h,-k,-l could have different intensities due to anomalous scattering effects.
MERGE=TRUE means that symmetry equivalent reflections are merged in the output file. The parameter is optional and MERGE=TRUE by default. Program packages like SHELX encourage the use of unmerged data and in this case MERGE=FALSE could be specified. Clearly, this program option has only the desired effect if the input data have not already been merged by xscale (use MERGE=FALSE in xscale).

Example
OUTPUT_FILE=myo.fobs CNS FRIEDEL'S_LAW=FALSE MERGE=TRUE
This specifies an output file, named myo.fobs, in the format required by the CNS structure analysis package. Friedels's law does not hold due to the presence of anomalous scatterers in the crystal. Symmetry equivalent reflections are merged, but reflections h, k, l and -h,-k,-l will appear separate on the output file.

GENERATE_FRACTION_OF_TEST_REFLECTIONS=

This (optional) parameter allows to select and mark a fraction of reflections from the input file as belonging to the test-set (used for computing R-free in CNS or SHELX). If a reflections is selected for the test-set, all symmetry related reflections and their Friedel mates are included also regardless whether Friedel's law holds true or not.

Test reflections are generated only if they are at a resolution outside the range covered by the file specified in INHERIT_TEST_REFLECTIONS_FROM_FILE=. This allows to keep previously defined test-reflections in case new data at higher resolution become available. New test-reflections are then selected only from the additional reflections.

Example
GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05
XDSCONV will sort all unique reflections by resolution and mark every 20th by a test-flag.

INHERIT_TEST_REFLECTIONS_FROM_FILE=

This (optional) parameter consists of a file name and a format identifier of the refinement program package which used the file. This parameter allows you to inherit a previously used test-set of reflections. XDSCONV takes care of possibly different conventions for specifying unique indices and does not require any specific order of the reflections in the file. This simplifies the use of different packages for structure determination as identical test-reflections can be used for reporting R-free troughout the refinement process. In addition, XDSCONV allows to inherit old test- reflections as well as to generate additional ones in the resolution region not covered by the old test reflections.

INHERIT_FRACTION_OF_TEST_REFLECTIONS=

This (optional) parameter allows to inherit only a fraction of the test-reflections. This option may be useful when you later realize that your original test-set is unnecessarily large. However, default is to keep them all (1.0) and in this case the parameter may be omitted.

Example
INHERIT_TEST_REFLECTIONS_FROM_FILE=myo.hkl SHELX
INHERIT_FRACTION_OF_TEST_REFLECTIONS=0.5
The new output file will inherit half of the old test-reflections from file myo.hkl used by the SHELX package.

WILSON_STATISTICS=

This optional parameter specifies whether the intensity data should obey Wilson statistics or not. The default of TRUE is almost always a good assumption, except for some exotic cases indicated by the parameter value FALSE. In these rare cases a truncated normal distribution instead of a Wilson disribution is used as a prior guess for estimating structure factor amplitudes. This results in a smaller number of rejected reflections.

Wolfgang Kabsch 
page last updated: October 6, 2003