xia2.multiplex¶
Introduction¶
xia2.multiplex performs symmetry analysis, scaling and merging of multi-crystal data sets, as well as analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferred orientation.
It uses a number of DIALS programs internally, including dials.cosym, dials.two_theta_refine, dials.scale and dials.symmetry:
Preliminary filtering of datasets using hierarchical unit cell clustering
Laue group determination and resolution of indexing ambiguities with dials.cosym
Determination of “best” overall unit cell with dials.two_theta_refine
Initial round of scaling with dials.scale
Estimation of resolution limit with dials.estimate_resolution
Final round of scaling after application of the resolution limit
Analysis of systematic absences with dials.symmetry
Optional ΔCC½ filtering to remove outlier data sets
Analysis of non-isomorphism, radiation damage and preferred orientation
Examples use cases¶
Multiple integrated experiments and reflections in combined files:
xia2.multiplex integrated.expt integrated.refl
Integrated experiments and reflections in separate input files:
xia2.multiplex integrated_1.expt integrated_1.refl \
integrated_2.expt integrated_2.refl
Override the automatic space group determination and resolution estimation:
xia2.multiplex space_group=C2 resolution.d_min=2.5 \
integrated_1.expt integrated_1.refl \
integrated_2.expt integrated_2.refl
Filter potential outlier data sets using the ΔCC½ method:
xia2.multiplex filtering.method=deltacchalf \
integrated.expt integrated.refl
Basic parameters¶
unit_cell_clustering {
threshold = 5000
log = False
}
scaling {
anomalous = False
brotation.spacing = None
secondary {
}
model = physical dose_decay array KB *auto
outlier_rejection = simple standard
min_partiality = None
partiality_cutoff = None
reflection_selection {
method = quasi_random intensity_ranges use_all random
Isigma_range = None
}
}
symmetry {
resolve_indexing_ambiguity = True
cosym {
normalisation = kernel quasi *ml_iso ml_aniso
d_min = Auto
min_i_mean_over_sigma_mean = 4
min_cc_half = 0.6
lattice_group = None
space_group = None
lattice_symmetry_max_delta = 5.0
best_monoclinic_beta = False
dimensions = Auto
use_curvatures = True
weights = count standard_error
min_pairs = 3
minimization {
engine = *scitbx scipy
max_iterations = 100
max_calls = None
}
}
laue_group = None
space_group = None
}
resolution {
d_max = None
d_min = None
cc_half_method = half_dataset *sigma_tau
reflections_per_bin = 10
labels = None
reference = None
emax = 4
}
rescale_after_resolution_cutoff = False
filtering {
method = None deltacchalf
deltacchalf {
max_cycles = None
max_percent_removed = None
min_completeness = None
mode = dataset image_group
group_size = None
stdcutoff = None
}
}
multi_crystal_analysis {
unit_cell = None
n_bins = 20
d_min = None
batch {
id = None
range = None
}
}
unit_cell {
refine = *two_theta
}
two_theta_refine {
combine_crystal_models = True
}
min_completeness = None
min_multiplicity = None
max_clusters = None
cluster_method = *cos_angle correlation unit_cell
identifiers = None
dose = None
nproc = Auto
remove_profile_fitting_failures = True
seed = 42
output {
log = xia2.multiplex.log
}
Full parameter definitions¶
unit_cell_clustering {
threshold = 5000
.help = "Threshold value for the clustering"
.type = float(value_min=0, allow_none=True)
log = False
.help = "Display the dendrogram with a log scale"
.type = bool
}
scaling {
anomalous = False
.help = "Separate anomalous pairs in scaling and error model optimisation."
.type = bool
rotation.spacing = None
.short_caption = "Interval (in degrees) between scale factors on rotation"
"axis"
.type = int(allow_none=True)
.expert_level = 2
brotation.spacing = None
.short_caption = "Interval (in degrees) between B-factors on rotation axis"
.type = int(allow_none=True)
secondary {
lmax = 0
.short_caption = "Number of spherical harmonics for absorption"
"correction"
.type = int(allow_none=True)
.expert_level = 2
share.absorption = False
.short_caption = "Apply a shared absorption correction between sweeps."
"Only suitable for scaling measurements from a single"
"crystal."
.type = bool
.expert_level = 2
}
absorption_level = low medium high
.short_caption = "Set the extent of absorption correction in scaling"
.type = choice
.expert_level = 2
model = physical dose_decay array KB *auto
.type = choice
outlier_rejection = simple standard
.type = choice
min_partiality = None
.type = float(value_min=0, value_max=1, allow_none=True)
partiality_cutoff = None
.type = float(value_min=0, value_max=1, allow_none=True)
reflection_selection {
method = quasi_random intensity_ranges use_all random
.help = "Method to use when choosing a reflection subset for scaling"
"model minimisation. The quasi_random option randomly selects"
"reflections groups within a dataset, and also selects groups"
"which have good connectedness across datasets for multi-dataset"
"cases. The random option selects reflection groups randomly for"
"both single and multi dataset scaling, so for a single dataset"
"quasi_random == random. The intensity_ranges option uses the"
"E2_range, Isigma_range and d_range options to the subset of"
"reflections The use_all option uses all suitable reflections,"
"which may be slow for large datasets."
.type = choice
Isigma_range = None
.type = floats(size=2)
}
}
symmetry {
resolve_indexing_ambiguity = True
.type = bool
cosym {
normalisation = kernel quasi *ml_iso ml_aniso
.type = choice
d_min = Auto
.type = float(value_min=0, allow_none=True)
min_i_mean_over_sigma_mean = 4
.type = float(value_min=0, allow_none=True)
min_cc_half = 0.6
.type = float(value_min=0, value_max=1, allow_none=True)
lattice_group = None
.type = space_group
space_group = None
.type = space_group
lattice_symmetry_max_delta = 5.0
.type = float(value_min=0, allow_none=True)
best_monoclinic_beta = False
.help = "If True, then for monoclinic centered cells, I2 will be"
"preferred over C2 if it gives a less oblique cell (i.e. smaller"
"beta angle)."
.type = bool
dimensions = Auto
.type = int(value_min=2, allow_none=True)
use_curvatures = True
.type = bool
weights = count standard_error
.type = choice
min_pairs = 3
.help = "Minimum number of pairs for inclusion of correlation"
"coefficient in calculation of Rij matrix."
.type = int(value_min=1, allow_none=True)
minimization {
engine = *scitbx scipy
.type = choice
max_iterations = 100
.type = int(value_min=0, allow_none=True)
max_calls = None
.type = int(value_min=0, allow_none=True)
}
}
laue_group = None
.help = "Specify the Laue group. If None, then the Laue group will be"
"determined by dials.cosym."
.type = space_group
space_group = None
.help = "Specify the space group. If None, then the dials.symmetry will"
"perform analysis of systematically absent reflections to"
"determine the space group."
.type = space_group
}
resolution
.short_caption = Resolution
{
d_max = None
.help = "Low resolution cutoff."
.short_caption = "Low resolution cutoff"
.type = float(value_min=0, allow_none=True)
d_min = None
.help = "High resolution cutoff."
.short_caption = "High resolution cutoff"
.type = float(value_min=0, allow_none=True)
rmerge = None
.help = "Maximum value of Rmerge in the outer resolution shell"
.short_caption = "Outer shell Rmerge"
.type = float(value_min=0, allow_none=True)
.expert_level = 1
completeness = None
.help = "Minimum completeness in the outer resolution shell"
.short_caption = "Outer shell completeness"
.type = float(value_min=0, allow_none=True)
.expert_level = 1
cc_ref = 0.1
.help = "Minimum value of CC vs reference data set in the outer resolution"
"shell"
.short_caption = "Outer shell CCref"
.type = float(value_min=0, allow_none=True)
.expert_level = 1
cc_half = 0.3
.help = "Minimum value of CC½ in the outer resolution shell"
.short_caption = "Outer shell CC½"
.type = float(value_min=0, allow_none=True)
.expert_level = 1
cc_half_method = half_dataset *sigma_tau
.type = choice
cc_half_significance_level = 0.1
.type = float(value_min=0, value_max=1, allow_none=True)
.expert_level = 1
cc_half_fit = polynomial *tanh
.type = choice
.expert_level = 1
isigma = None
.help = "Minimum value of the unmerged <I/sigI> in the outer resolution"
"shell"
.short_caption = "Outer shell unmerged <I/sigI>"
.type = float(value_min=0, allow_none=True)
.expert_level = 1
misigma = None
.help = "Minimum value of the merged <I/sigI> in the outer resolution"
"shell"
.short_caption = "Outer shell merged <I/sigI>"
.type = float(value_min=0, allow_none=True)
.expert_level = 1
i_mean_over_sigma_mean = None
.help = "Minimum value of the unmerged <I>/<sigI> in the outer resolution"
"shell"
.short_caption = "Outer shell unmerged <I>/<sigI>"
.type = float(value_min=0, allow_none=True)
.expert_level = 2
nbins = 100
.help = "Maximum number of resolution bins to use for estimation of"
"resolution limit."
.short_caption = "Number of resolution bins."
.type = int(allow_none=True)
.expert_level = 1
reflections_per_bin = 10
.help = "Minimum number of reflections per bin."
.type = int(allow_none=True)
binning_method = *counting_sorted volume
.help = "Use equal-volume bins or bins with approximately equal numbers of"
"reflections per bin."
.short_caption = "Equal-volume or equal #ref binning."
.type = choice
.expert_level = 1
anomalous = False
.short_caption = "Keep anomalous pairs separate in merging statistics"
.type = bool
.expert_level = 1
labels = None
.type = strings
space_group = None
.type = space_group
.expert_level = 1
reference = None
.type = path
emax = 4
.help = "Reject reflecitons with normalised intensities E^2 > emax^2"
.type = float(value_min=0, allow_none=True)
}
rescale_after_resolution_cutoff = False
.help = "Re-scale the data after application of a resolution cutoff"
.type = bool
filtering {
method = None deltacchalf
.help = "Choice of whether to do any filtering cycles, default None."
.type = choice
deltacchalf {
max_cycles = None
.type = int(value_min=1, allow_none=True)
max_percent_removed = None
.type = float(allow_none=True)
min_completeness = None
.help = "Desired minimum completeness, as a percentage (0 - 100)."
.type = float(value_min=0, value_max=100, allow_none=True)
mode = dataset image_group
.help = "Perform analysis on whole datasets or batch groups"
.type = choice
group_size = None
.help = "The number of images to group together when calculating delta"
"cchalf in image_group mode"
.type = int(value_min=1, allow_none=True)
stdcutoff = None
.help = "Datasets with a ΔCC½ below (mean - stdcutoff*std) are removed"
.type = float(allow_none=True)
}
}
multi_crystal_analysis {
unit_cell = None
.type = unit_cell
n_bins = 20
.type = int(value_min=1, allow_none=True)
d_min = None
.type = float(value_min=0, allow_none=True)
batch
.multiple = True
{
id = None
.type = str
range = None
.type = ints(size=2, value_min=0)
}
}
unit_cell {
refine = *two_theta
.type = choice(multi=True)
}
two_theta_refine {
combine_crystal_models = True
.type = bool
}
min_completeness = None
.type = float(value_min=0, value_max=1, allow_none=True)
min_multiplicity = None
.type = float(value_min=0, allow_none=True)
max_clusters = None
.type = int(value_min=1, allow_none=True)
cluster_method = *cos_angle correlation unit_cell
.type = choice
identifiers = None
.type = strings
dose = None
.type = ints(size=2, value_min=0)
nproc = Auto
.help = "The number of processors to use"
.type = int(value_min=1, allow_none=True)
.expert_level = 0
remove_profile_fitting_failures = True
.type = bool
exclude_images = None
.help = "Input in the format exp:start:end Exclude a range of images (start,"
"stop) from the dataset with experiment identifier exp (inclusive"
"of frames start, stop)."
.type = strings
.multiple = True
.expert_level = 1
seed = 42
.type = int(value_min=0, allow_none=True)
output {
log = xia2.multiplex.log
.type = str
}
