3D visualization (ArtiaX)

nextPYP produces all the necessary files to visualize a refined structure mapped back into the original tomograms using the ArtiaX plugin for ChimeraX.

Download files

First, you need to download the following files to your local computer:

  • Tomogram reconstruction (*.rec)

  • Refined map (*.mrc)

  • Corresponding particle orientations (*.star)

You can get these files from nextPYP as follows:

  • Go to the Pre-processing` block, click on the Tilt-series tab, select a tilt-series using the navigation bar and go to the Tomogram section. Download the .rec file by clicking on the gray/green badge

  • Go to the Particle refinement block, select the Reconstruction tab and download the Cropped Map using the dropdown menu

  • In the same Particle refinement block, go the Metadata tab, type the name of the tilt-series in the box and click Search. Download the corresponding .star file by clicking on the gray/green badge

Display in ChimeraX

  • 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

  • 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

Tomogram from immature HIV-1 virions from EMPIAR-10164 showing with a high-resolution model of Gag mapped back into the tomogram.

Tip

  • Repeating this process for other tilt-series in the dataset is usually a good idea

  • 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