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/

Step 2: Load data into ChimeraX/ArtiaX

  • 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:

ArtiaX visualization of HIV1-Gag


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.