
Program documentation
=====================

Main processing commands:

.. toctree::
   :maxdepth: 1

   dials_import
   dials_find_spots
   dials_index
   dials_refine_bravais_settings
   dials_reindex
   dials_refine
   dials_integrate
   dials_two_theta_refine
   dials_cosym
   dials_symmetry
   dials_scale
   dials_export
   xia2_multiplex

Utilities:

.. toctree::
   :maxdepth: 1

   dials_show
   dials_image_viewer
   dials_reciprocal_lattice_viewer
   dials_generate_mask
   dials_check_indexing_symmetry
   dials_search_beam_position
   dials_report
   dials_plot_scan_varying_model
   dials_find_spots_server
   dials_find_spots_apache_server
   dials_apply_mask
   dials_create_profile_model
   dials_estimate_gain
   dials_estimate_resolution
   dials_predict
   dials_merge_cbf
   dials_export_bitmaps
   dials_slice_sequence
   dials_compare_orientation_matrices
   dials_spot_counts_per_image
   dials_stereographic_projection
   dials_combine_experiments
   dials_align_crystal
   dials_anvil_correction
   dials_missing_reflections
   dials_filter_reflections

Printable command line reference:

.. raw:: html

  <div class="embedpdf">
  <iframe src="https://drive.google.com/file/d/0B0yDAeP5vfI7aW5ORWdORHVmOGs/preview"
  width=100% height=100%>
  <p>It appears you don't have Adobe Reader or PDF support in this web browser. <a href="lorem.pdf">Click here to download the PDF</a>. Or <a href="http://get.adobe.com/reader/" target="_blank">click here to install Adobe Reader</a>.</p>
  </iframe>
  </div>
  <a class="reference external" href="https://drive.google.com/file/d/0B0yDAeP5vfI7aW5ORWdORHVmOGs/preview" target="_blank">Open pdf in new tab</a>


More details on most used DIALS algorithms:

.. raw:: html

  <iframe
    src="https://docs.google.com/presentation/d/e/2PACX-1vSDBwscFn3Y6wnRf5NXlEW1faBYToPOlkirc9ctJQ9TYf975Vh5qmbTofXb0jPtD7W3MixldFZxA_2C/embed?start=false&loop=false&delayms=3000"
    frameborder="0"
    width="960"
    height="749"
    mozallowfullscreen="true"
    webkitallowfullscreen="true">
  </iframe>
  <a class="reference external"
    href="https://docs.google.com/presentation/d/e/2PACX-1vSDBwscFn3Y6wnRf5NXlEW1faBYToPOlkirc9ctJQ9TYf975Vh5qmbTofXb0jPtD7W3MixldFZxA_2C/embed?start=false&loop=false&delayms=3000">Open presentation in new tab
  </a>
