Multiplex GUI

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

newsfragments/1969.doc

@@ -0,0 +1 @@
+Update some Cosym and resolution-related PHIL descriptions.

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
 """
 )

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"
@@ -374,25 +377,31 @@ 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."
     .short_caption = "Equal-volume or equal #ref binning."
     .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"
 """