Making Molecular Movies in ChimeraX

Tom Goddard
West Coast Protein Crystallography Workshop
March 20, 2017 (updated May 22, 2019; see original)

How to make movies showing molecular structures using ChimeraX. We will look at galactose binding protein as an example (PDB entries 3gbp and 2fw0).

Run Tutorial in ChimeraX

Open this web page within ChimeraX using the following ChimeraX command:

• open http://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html

This will display it in the ChimeraX browser, and then clicking on the commands in the tutorial will run the commands.

Spin Movie

Spin a molecule 360° and record a movie.

• Open galactose binding protein:
• open 3gbp

• Use white background and black outlines (silhouettes):
• Command preset pub or click toolbar icons

• Record a spin movie1.mp4 to the desktop:
• Click toolbar icon

Zone around galactose ligand

Show the binding site in more detail.

• Hide the ribbon:
• Command hide ribbon or click toolbar icon

• Hide atoms far from ligand.
• Hold ctrl key and drag a box around far atoms to select them.
• Command hide sel or click toolbar icon

• Make the ligand stand out using sphere style and color:
• select ligand
• style sel sphere or click toolbar icon
• select clear or hold ctrl key and click on background
• color ligand & C pink

• Rock binding site back and forth:
• turn y 25 300 rock 150

• Record movie with 4 commands on one line separated by semicolons:
• movie record ; turn y 25 300 rock 150 ; wait 300 ; movie encode ~/Desktop/movie2.mp4

X-ray density near galactose ligand

Look at x-ray density in binding site.

• Return to black background without silhouettes:
• Command preset interactive or click toolbar icons

• Open x-ray map:
• open 3gbp from eds

• Set contour level:
• vol #2 level 0.5

• Limit map display to near the galactose ligand:
• surface zone #2 near ligand dist 8

• Show ligand in ball-and-stick style:
• style ligand ball

Show fit of each residue in density

• Start the Residue Fit tool to show how well each residue fits in map:
• resfit #1 map #2

• Move the slider or use the play button ▶ in the ChimeraX interface to step through the residues; click the record button to make a movie resfit.mp4 (on Desktop) showing each residue in sequence; click to stop recording before the entire structure is done.

Morph between bound and unbound conformation

• Close the density map:
• close #2

• Change back to the original display with ribbons:
• preset original

• Open galactose binding protein in unbound state:
• open 2fw0

• Put both structures in view:
• view or click toolbar icon

• Align the unbound structure to the bound structure:
• matchmaker #2 to #1
• view or click toolbar icon

• Calculate an interpolation between two conformations:
• morph #1,2

• Replay the morph in both directions:
• coordset #3 1,21 ; wait 21 ; coordset #3 21,1

• Show just the galactose from the bound structure:
• show #1 model
• hide #1 atoms,ribbons
• show #1 & ligand & ~ H

• Show residues in morph near ligand:
• select zone ligand 5 #3 residues true
• show sel
• select clear

• Use white background and silhouette edges:
• Command preset pub or click toolbar icons

• Put movie recording commands in a plain text file on Desktop gbpmovie.cxc:

• movie record supersample 3
  coordset #3 1,21
  wait 40
  coordset #3 21,1
  wait 40
  movie encode ~/Desktop/movie3.mp4 quality high
  

• Run commands by opening command file:
• open ~/Desktop/gbpmovie.cxc

• ...or type them on a single line:
• movie record ; coordset...

Virtual reality view of binding site

Create a 360° stereoscopic scene on YouTube for viewing in virtual reality headsets. Example scene to view with cellphone YouTube app and VR headset: GWRGc7jpX8g

• Close all models and reopen galactose binding protein:
• close
• open 3gbp

• Switch to 360° camera mode showing 0–360° longitude and –90 to 90° latitude, where top half is left eye, bottom half is right eye:
• camera 360tb eyeSeparation 0.05

• Make window aspect ratio 1 to 1:
• windowsize 600 600

• Center, zoom in, and set center of rotation (cofr) at ligand:
• view
• zoom 15
• cofr ligand

• Record a movie at high resolution with no motion:
• movie record size 4096,4096 ; wait 5 ; movie encode ~/Desktop/gbp.mp4 framerate 1

• Add header info to the movie specifying 360° top-bottom format by running the YouTube 360 Video Metadata program.
• 1) Use your normal computer web browser and Google for youtube upload virtual reality.
• 2) Download the 360 Video Metadata app under the Prepare for upload section. (The ChimeraX browser does not handle download links.)
• 3) Run the program, opening gpb.mp4, enabling “My video is spherical” and “My video is stereoscopic” to make file gbp_injected.mp4.

• Upload your video to YouTube. Requires a Google account.
• 1) Use the YouTube upload page in your normal computer web browser.

• View the video on YouTube using cellphone and VR headset.
• 1) Install the YouTube app on your cellphone.
• 2) Open your video in the YouTube app using the URL assigned during upload.
• 3) Tap the eye-glasses mask icon at the bottom of the video to enter VR mode.
• 4) Put cellphone into VR headset, e.g. Google Cardboard.