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