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Updates for the small molecule tutorial (dials#2692)
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* Fix error in text - wrong viewer
* Add note about dials.symmetry catering more for MX
* Use dials.export format=shelx
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dagewa committed Jul 31, 2024
1 parent b9d3fd4 commit b6bd348
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15 changes: 6 additions & 9 deletions doc/sphinx/documentation/tutorials/small_molecule_tutorial.rst
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Expand Up @@ -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
Expand All @@ -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
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Expand Down Expand Up @@ -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
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1 change: 1 addition & 0 deletions newsfragments/2692.bugfix
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Improvements to the small molecule tutorial.

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