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ChimeraX (and ArtiaX) Visualization

Using ChimeraX with the ArtiaX Plugin and our quantified surfaces, we will make a (hopefully attractive) visualization of our data. We'll do this on the work machines, but it will feel MUCH snappier on your home workstation!

Setup

  1. Start ChimeraX with module load chimera && chimerax
  2. Install ArtiaX: Tools -> More tools to get to the toolshed, then search and install ArtiaX. Restart ChimeraX to activate ArtiaX!
  3. Download the star file: clean_ribosomes.star. ArtiaX has a (new as of a couple weeks ago) open bug with starfiles with strings in it, so I am just providing a clean starfile for you. I made it with the starfile python repository

Making the right obj/mtl combo:

Here, we'll export an obj file with a specific color map using morphometrics:

morphometrics export_obj --feature IMM_dist config.yml morphometrics/YTC041_1_lam4_2_ts_002_labels_OMM.AVV_rh9.vtp

This will make an obj file with an associated mtl (material) file, which records color for the obj in a way that lots of different softwares read.

Make that figure!

  1. Load the obj file with chimeraX
  2. Launch ArtiaX
  3. Add clean_ribosomes.star to the artiaX particle lists
  4. Go to Select/Manipulate and set the Pixel Size factors to 3.3,1
  5. Add your raw tomogram to the artiaX tomogram list
  6. Under tomograms menu, average 5 slabs.
  7. Choose the orthoslice you want, near the edge - or hide it altogether!
  8. Fetch EMDB-48752!
  9. Under visualization, add new surface, and choose 48752.
  10. Enable soft lighting
  11. Take pictures, enjoy!