Merge remote-tracking branch 'upstream/main' into tof_scaling

toastisme · Aug 19, 2024 · 159f56d · 159f56d
2 parents 76f3112 + a2f8f71
commit 159f56d
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diff --git a/.conda-envs/linux.txt b/.conda-envs/linux.txt
@@ -33,6 +33,7 @@ conda-forge::pint
 conda-forge::pip
 conda-forge::psutil
 conda-forge::pybind11
+conda-forge::pyopengl
 conda-forge::pyrtf
 conda-forge::pytest
 conda-forge::pytest-forked

diff --git a/.conda-envs/macos.txt b/.conda-envs/macos.txt
@@ -33,6 +33,7 @@ conda-forge::pip
 conda-forge::psutil
 conda-forge::pthread-stubs
 conda-forge::pybind11
+conda-forge::pyopengl
 conda-forge::pyrtf
 conda-forge::pytest
 conda-forge::pytest-forked

diff --git a/.conda-envs/windows.txt b/.conda-envs/windows.txt
@@ -31,6 +31,7 @@ conda-forge::pint
 conda-forge::pip
 conda-forge::psutil
 conda-forge::pybind11
+conda-forge::pyopengl
 conda-forge::pyrtf
 conda-forge::pytest
 conda-forge::pytest-forked

diff --git a/doc/sphinx/documentation/tutorials/small_molecule_tutorial.rst b/doc/sphinx/documentation/tutorials/small_molecule_tutorial.rst
@@ -117,7 +117,7 @@ which will integrate each sweep in sequence, again using all available cores. Af
 
 .. code-block:: bash
 
- dials.reciprocal_lattice_viewer integrated.refl integrated.expt
+ dials.image_viewer integrated.refl integrated.expt
 
 
 
@@ -132,6 +132,8 @@ So far the data were processed with a triclinic unit cell, which is usually OK b
 
 This will look at the shape of the unit cell and determine the maximum possible symmetry based on the cell parameters, with some tolerance. Each of the possible symmetry operations will be individually tested and scored, and those operations identified as being present will be composed into the point group to be assigned to the data. An attempt is then made to estimate the space group from the presence or absence of axial reflections: this is rather less reliable than the point group determination but also less important for the scaling. After the point group has been determined the reflections will be reindexed automatically to match the correct setting, ensuring that the data are correctly prepared for scaling.
 
+.. note:: ``dials.symmetry`` will only suggest one of the 65 Sohncke space groups relevant for chiral molecules. It will not detect mirrors or glide planes.
+
 
 Scaling
 -------
@@ -225,19 +227,14 @@ However these may be useful in later structure refinement.
 Exporting
 ---------
 
-The output data are by default saved in the standard DIALS reflection format, which is not particularly useful. In MX, a standard format is MTZ which includes the unit cell and symmetry information with the reflection data. This is created with
+The output data are by default saved in the standard DIALS reflection format, which is not particularly useful. DIALS is able to convert this to SHELX format though. This can be done by
 
 .. code-block:: bash
 
- dials.export scaled.refl scaled.expt
-
-And there is a useful "jiffy" included with xia2 to convert this to SHELX format and generate .ins and .hkl files for structure solution and refinement viz:
-
-.. code-block:: bash
+ dials.export scaled.refl scaled.expt format=shelx shelx.ins=lcys.ins shelx.hklout=lcys.hkl composition=CHNOS
 
- xia2.to_shelx scaled.mtz lcys CHNOS
 
-Such that you can then run
+So that you can then run
 
 .. code-block:: bash
 

diff --git a/newsfragments/2688.bugfix b/newsfragments/2688.bugfix
@@ -0,0 +1 @@
+Avoid deprecated ``matplotlib.cm.get_cmap`` calls
diff --git a/newsfragments/2692.bugfix b/newsfragments/2692.bugfix
@@ -0,0 +1 @@
+Improvements to the small molecule tutorial.
diff --git a/newsfragments/2696.feature b/newsfragments/2696.feature
@@ -0,0 +1 @@
+``dials.symmetry``: allow free selection of ``significance_level`` in the range [0,1]
diff --git a/newsfragments/2700.bugfix b/newsfragments/2700.bugfix
@@ -0,0 +1,2 @@
+``dials.merge``: Use gemmi to output merged MTZs for consistency with ``dials.export``
+
diff --git a/newsfragments/2707.bugfix b/newsfragments/2707.bugfix
@@ -0,0 +1 @@
+``dials.reciprocal_lattice_viewer``: fix middle mouse drag to translate function.
diff --git a/newsfragments/2709.feature b/newsfragments/2709.feature
@@ -0,0 +1 @@
+``dials.export``: Add support for exporting still data in mmcif format, that can be understood with gemmi
diff --git a/newsfragments/2714.misc b/newsfragments/2714.misc
@@ -0,0 +1,2 @@
+Tidy output of ``dials.index`` around the defaults for ``joint_index``
+
diff --git a/newsfragments/2715.bugfix b/newsfragments/2715.bugfix
@@ -0,0 +1 @@
+Modified branching to Laue refinement methods to check for ExperimentType first.
diff --git a/newsfragments/2718.bugfix b/newsfragments/2718.bugfix
@@ -0,0 +1,3 @@
+Performance improvement for selections from large reflection tables. For a
+table containing 165k experiment identifiers the speedup is 1000x (12 minutes
+per call).