================================
Visualization in ChimeraX/ArtiaX
================================

``nextPYP`` produces all the necessary files to visualize a refined map into the original tomogram positions using ChimeraX/ArtiaX.

Step 1: Download the necessary files
------------------------------------

Select the refinement block where you will extract the particle locations from. Click on the ``Edit`` menu for that block and select the ``Show filesystem location`` to find out the location of the project in the filesystem.

From this location, you will need to download the following files to your local computer:

- Tomogram reconstruction (``mrc/tile_series_name.rec``)
- Refined map (``frealign/maps/block_name_r{class_number}_{iteration_number}_crop.mrc``)
- Corresponding particle orientations (``frealign/artiax/tile_series_name_K1.star``)

Step 2: Load data into ChimeraX/ArtiaX
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- Open ChimeraX (we assume the ArtiaX plugin is already installed)
- Open the tomogram file ``tilt_series_name.rec``
- Run the following commands in the ChimeraX shell:
   - ``volume permuteAxes #1 xzy``
   - ``volume flip #2 axis z`` (this step is only necessary when the dataset has virions)
- Go to the ArtiaX tab and ``Launch`` the plugin
- In the **Tomograms** section (main ArtiaX panel on the left), select model #3 (permuted z flip) from the ``Add Model`` dropdown menu and click ``Add!``
- Go to to the ArtiaX options panel on the right, and set the ``Pixel Size`` for the **Current Tomogram** to the binned pixel size (10.8 for the EMPIAR-10164 tutorial) and click ``Apply``
- From the **Particles List** section (main ArtiaX panel on the left), select ``Open List ...`` and browse to the location of the ``.star`` file
- Go to the ArtiaX options panel on the right, select the **Select/Manipulate** tab and set the ``Origin`` of the ``Pixelsize Factors`` to the unbinned pixel size of the data (1.35 for the EMPIAR-10164 tutorial)
- From the **Geometric Models** section (main ArtiaX panel on the left), go to ``Open Geomodel ...`` and select the refined map
- Go to the ArtiaX options panel on the right, in the **Visualization** tab, set the ``Use Model`` from the dropdown menu to the refined map and click ``Attach Model``
- From the **Color Settings** section, select ``Colormap`` and choose the attribute ``rlnLogLikelihoodContribution`` from the dropdown menu

If everything went well, you should obtain a result similar to this:

.. figure:: ../images/guide_artiax_10164.webp
    :alt: ArtiaX visualization of HIV1-Gag

.. tip::

    Depending on the dimensions of the refined map and the number of particles in the tomogram, you may need to downsample the map to make ChimeraX more responsive.

.. seealso::

    * :doc:`Filter micrographs/tilt-series<filters>`
    * :doc:`Particle picking<picking>`
    * :doc:`Neural-network picking<neural_network>`
    * :doc:`Overview<overview>`