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docs/dsr.rst

@@ -109,45 +109,53 @@ Since version 181, `ShelXle <http://www.shelxle.org>`_
 has the ability to start a graphical user interface for DSR. A mouse
 click on *Tools*--\> *DSR plugin* will start the DSR GUI:
 
-![](/Users/daniel/Documents/GitHub/DSR/docs/images/media/image1.png){width="6.166666666666667in"
-height="0.6959995625546807in"}
+.. image:: images/media/image1.png
+  :width: 100%
+  :alt: Start plugin
 
-![](/Users/daniel/Documents/GitHub/DSR/docs/images/media/image2.tiff){width="4.0779921259842515in"
-height="3.6771489501312336in"}
+.. image:: images/media/image2.png
+  :width: 100%
+  :alt: DSR Window
 
-Now you need to select a fragment in the list. The list of fragments can
-be shortened via the search field.
+
+Now you need to select a fragment in the list. The list of fragments
+can be searched using the search field. The search shortens the list
+to the fragments that best match by name.
 
 To fit a fragment into the structure in ShelXle, select three
 atoms/Q-peaks in the target molecule (with a left mouse click while
 holding STRG) and the fragments 3D view (just left mouse click) each.
 The 3D view should now show a preview of the fitted fragment:
 
-![](/Users/daniel/Documents/GitHub/DSR/docs/images/media/image3.png){width="2.4102449693788275in"
-height="2.256988188976378in"}
+.. image:: images/media/image3.png
+  :width: 100%
+  :alt: Fragment fit
 
 You can now control all the features of DSR with the options menu below:
 
-![](/Users/daniel/Documents/GitHub/DSR/docs/images/media/image4.tiff){width="6.071395450568679in"
-height="1.2321544181977253in"}
+.. image:: images/media/image4.png
+  :width: 100%
+  :alt: Options
 
 Setting PART to zero will disable them. The residue number will always
 be chosen as the next free available. You can safely leave this as it is
 or change the residue name.
 
 The "Free variable" option defines the free variable for the fragment
 occupation in SHELXL. The Free variable will be combined with the
-occupation option. For example a free variable of -3 and an occupation
-of 1 will be combined to -31. The result appears instantly in the output
+occupation option. For example a free variable of --3 and an occupation
+of 1 will be combined to --31. The result appears instantly in the output
 window.
 
 "External restraints" writes the restraints to an external file.
 
 "Calculate DFIX" automatically generates DFIX/DANG/FLAT restraints from
-the geometry of the fragment.
+the geometry of the fragment. This can be particular useful to stabilize
+the a fragment on special positions.
 
-![](/Users/daniel/Documents/GitHub/DSR/docs/images/media/image5.png){width="4.8909492563429575in"
-height="3.4003762029746283in"}
+.. image:: images/media/image5.png
+  :width: 100%
+  :alt: Start plugin
 
 To create or edit a fragment, click on \"Edit fragment\". The edit
 window allows adding, updating and deleting of fragments.