XDSCONV: Input Parameters

All input parameters 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


INPUT_FILE=

This parameter specifies the reflection data that XDSCONV should convert. Usually, this file has been generated previously by the scaling program xscale. The parameter comprises 2 values: file name and file format.

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 (optional)
can be XDS_ASCII or the outdated formats ANOMAL, NORMAL, OLDHKL, UNIQUE. If file format is omitted, XDS_ASCII is assumed by default.
XDS_ASCII
is the reflection file format now being generated and used within the xds-package. All other formats listed below are outdated since August 2000.
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the outdated format refers to files ANOMAL.HKL that were used by the old versions of the xds-package for representing anomalous scattering intensity data.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these outdated formats refers to files NORMAL.HKL that were used by the old versions of the xds-package for representing unique intensities in the absence of anomalous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the outdated format refers to files UNIQUE.HKL that were used by the old versions of the xds-package before November 1998.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.

Example
INPUT_FILE=../XSCALE.HKL
This specifies an input file, named ../XSCALE.HKL. The file format is assumed to be XDS_ASCII by default.


INCLUDE_RESOLUTION_RANGE=

Reflection h, k, l from the input file is accepted only if its resolution d(h,k,l)=λ/{2sinθ} is within the specified range. If omitted all reflections are accepted.

Example
INCLUDE_RESOLUTION_RANGE= 20.0 3.0
Reflections with a resolution between the low resolution limit (20.0 Å) and the high resolution limit (3.0 Å) are accepted.


OUTPUT_FILE=

This parameter specifies the converted output file for subsequent use by various crystal structure analysis packages. The parameter comprises 2 values: File name, File format.

File name
is the name assigned to the output file. The name should not exceed 50 characters in length. Intervening blanks or exclamation marks are not allowed.
File format
can be: CCP4 CCP4_F CCP4_I CCP4_I+F CNS SHELX XtalView

Example
OUTPUT_FILE=myo.fobs CNS
This specifies an output file, named myo.fobs, in the format required by the CNS structure analysis package.


FRIEDEL'S_LAW=

FRIEDEL'S_LAW=TRUE if reflections h, k, l and -h,-k,-l are expected to 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.
The parameter is mandatory: its value is taken from the header of the input file unless specified explicitly by the user in XDSCONV.INP.


MERGE=

MERGE=TRUE means that the weighted mean of symmetry equivalent reflection intensities appearing in the input file will be determined and used in the output file. The parameter is optional and MERGE=TRUE by default. At present, MERGE=TRUE is enforced by XDSCONV for all output file formats other than CNS and SHELX. 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 reflection 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 provides a possibility to inherit a previously used test-set of reflections so that identical test-reflections can be used for reporting R-free troughout the various stages of a structure refinement process. The parameter comprises 2 values: File name, File format.

File name
is the name of the file from which test reflections should be taken. The name should not exceed 50 characters in length. Intervening blanks or exclamation marks are not allowed.
File format
at present this must be: CNS SHELX

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.


NEGATIVE_INTENSITY_CUTOFF=

This optional parameter defines the minimum acceptable I/sigma(I) value for input reflections. In case of more than one symmetry related input reflection, their weighted mean intensity and corresponding standard deviation are used for the test. If the Imean/sigma(Imean) ratio falls below the specified negative intensity cut-off ratio all of these reflections will be ignored. Note, that Friedel pairs are not considered symmetry related if FRIEDEL'S_LAW=FALSE.

Example
NEGATIVE_INTENSITY_CUTOFF=-3
This is the default.


SPACE_GROUP_NUMBER=

Space-group number of the crystal. The numbers corresponding to each of the 230 possible space group are defined in the "INTERNATIONAL TABLES I" together with a standard set of symmetry operators. If several choices exist XDSCONV selects the appropriate set of operators according to the unit cell constants provided by the user. The parameter is mandatory and extracted from the header of the input file unless specified explicitly by the user in XDSCONV.INP.

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


UNIT_CELL_CONSTANTS=

Unit cell parameters a, b, c (Å) and α, β, γ (°). The cell constants must meet the geometrical requirements implicated by the space group symmetry. First and second setting of monoclinic crystals must be distinguishable by the cell constants. The cell parameters are mandatory and extracted from the header of the input file unless specified explicitly by the user in XDSCONV.INP.

Example:
UNIT_CELL_CONSTANTS=125.9 125.9 144.7 90.0 90.0 90.0
SPACE_GROUP_NUMBER=77
This is an explicit specification of 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° as required by the space group. If these parameters were not given in XDSCONV.INP, they must be available from the header of the input file.


© 2008-2016, MPI for Medical Research, Heidelberg Imprint.
Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
page last updated: April 22, 2016