Repository : https://github.com/dials/dials
On branch : main
Link : https://github.com/dials/dials/commit/79c44473c2f9582873729cda11782912fecab147
commit 79c44473c2f9582873729cda11782912fecab147
Author: David Waterman <[log in to unmask]>
Date: Fri Jan 14 11:51:30 2022 +0000
Update some Cosym and resolution-related PHIL captions (#1969)
This helps the i2 xia2.multiplex GUI populate it's field descriptions.
Co-authored-by: Richard Gildea <[log in to unmask]>
79c44473c2f9582873729cda11782912fecab147
algorithms/symmetry/cosym/__init__.py | 17 ++++++++++++++++-
newsfragments/1969.doc | 1 +
util/exclude_images.py | 1 +
util/resolution_analysis.py | 13 +++++++++++--
4 files changed, 29 insertions(+), 3 deletions(-)
diff --git a/algorithms/symmetry/cosym/__init__.py b/algorithms/symmetry/cosym/__init__.py
index b9f7d7c56..e1da897c4 100644
--- a/algorithms/symmetry/cosym/__init__.py
+++ b/algorithms/symmetry/cosym/__init__.py
@@ -40,44 +40,59 @@
min_i_mean_over_sigma_mean = 4
.type = float(value_min=0)
+ .short_caption = "Minimum <I>/<σ>"
min_cc_half = 0.6
.type = float(value_min=0, value_max=1)
+ .short_caption = "Minimum CC½"
lattice_group = None
.type = space_group
+ .short_caption = "Lattice group"
space_group = None
.type = space_group
+ .short_caption = "Space group"
lattice_symmetry_max_delta = 5.0
.type = float(value_min=0)
+ .short_caption = "Lattice symmetry max δ"
best_monoclinic_beta = True
.type = bool
.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)."
+ .short_caption = "Best monoclinic β"
dimensions = Auto
.type = int(value_min=2)
+ .short_caption = "Dimensions"
use_curvatures = True
.type = bool
+ .short_caption = "Use curvatures"
weights = count standard_error
.type = choice
+ .short_caption = "Weights"
min_pairs = 3
.type = int(value_min=1)
.help = 'Minimum number of pairs for inclusion of correlation coefficient in calculation of Rij matrix.'
+ .short_caption = "Minimum number of pairs"
-minimization {
+minimization
+ .short_caption = "Minimization"
+{
engine = *scitbx scipy
.type = choice
+ .short_caption = "Engine"
max_iterations = 100
.type = int(value_min=0)
+ .short_caption = "Maximum number of iterations"
max_calls = None
.type = int(value_min=0)
+ .short_caption = "Maximum number of calls"
}
nproc = None
diff --git a/newsfragments/1969.doc b/newsfragments/1969.doc
new file mode 100644
index 000000000..958577d59
--- /dev/null
+++ b/newsfragments/1969.doc
@@ -0,0 +1 @@
+Update some Cosym and resolution-related PHIL descriptions.
diff --git a/util/exclude_images.py b/util/exclude_images.py
index 052f82a97..a66bd2912 100644
--- a/util/exclude_images.py
+++ b/util/exclude_images.py
@@ -18,6 +18,7 @@
.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)."
+ .short_caption = "Exclude images"
.expert_level = 1
"""
)
diff --git a/util/resolution_analysis.py b/util/resolution_analysis.py
index 3ee4568de..b86fe4b04 100644
--- a/util/resolution_analysis.py
+++ b/util/resolution_analysis.py
@@ -345,12 +345,15 @@ def miller_array_from_mtz(unmerged_mtz, anomalous=False, labels=None):
.expert_level = 1
cc_half_method = *half_dataset sigma_tau
.type = choice
+ .short_caption = "CC½ method"
cc_half_significance_level = 0.1
.type = float(value_min=0, value_max=1)
.expert_level = 1
+ .short_caption = "CC½ significance level"
cc_half_fit = polynomial *tanh
.type = choice
.expert_level = 1
+ .short_caption = "CC½ fit"
isigma = None
.type = float(value_min=0)
.help = "Minimum value of the unmerged <I/sigI> in the outer resolution shell"
@@ -374,6 +377,7 @@ def miller_array_from_mtz(unmerged_mtz, anomalous=False, labels=None):
reflections_per_bin = 10
.type = int
.help = "Minimum number of reflections per bin."
+ .short_caption = "Minimum number of reflections per bin"
binning_method = *counting_sorted volume
.type = choice
.help = "Use equal-volume bins or bins with approximately equal numbers of reflections per bin."
@@ -381,18 +385,23 @@ def miller_array_from_mtz(unmerged_mtz, anomalous=False, labels=None):
.expert_level = 1
anomalous = False
.type = bool
- .short_caption = "Keep anomalous pairs separate in merging statistics"
+ .help = "Keep anomalous pairs separate in merging statistics"
+ .short_caption = "Anomalous"
.expert_level = 1
labels = None
.type = strings
+ .short_caption = "Labels"
space_group = None
.type = space_group
.expert_level = 1
+ .short_caption = "Space group"
reference = None
.type = path
+ .short_caption = "Reference"
emax = 4
.type = float(value_min = 0)
- .help = "Reject reflecitons with normalised intensities E^2 > emax^2"
+ .help = "Reject reflections with normalised intensities E^2 > emax^2"
+ .short_caption = "Maximum normalised intensity"
"""
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