Making Molecular Movies in ChimeraX

Tom Goddard
West Coast Protein Crystallography Workshop
March 20, 2017

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.cgl.ucsf.edu/chimera/data/wcpcw-mar2017/moviemaking.html

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

1) Spin Movie

Spin a molecule 360 degrees and record a movie.

• Open galactose binding protein:
• open 3gbp

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

2) Zone around galactose ligand

Show the binding site in more detail.

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

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

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

• Set center of rotation at center of ligand:
• cofr ligand

• Rock binding site back and forth:
• turn y 0.5 rock 100
• stop

• Record movie with 4 commands on one line separated by semicolons:
• movie record ; turn y 0.5 rock 100 ; wait 300 ; movie encode ~/Desktop/movie2.mp4

3) X-ray density near galactose ligand

Look at x-ray density in binding site.

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

• Set contour level:
• vol #2 level 0.5

• Show map only near galactose ligand:
• surface zone #2 near ligand range 8

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

4) Show fit of each residue in density

• Start the Residue Fit tool to make movie showing how well each residue fits in map.
• resfit #1 map #2

• Press the record button to make a movie resfit.mp4 (on desktop) showing each residue in sequence, press to stop recording.

5) Morph between bound and unbound conformation

• Close the density map:
• close #2

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

• Zoom out and show all atoms of the bound structure
• view all or press toolbar icon
• show #1 ribbon

• Align the unbound structure to the bound structure:
• matchmaker #2 to #1

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

• Hide the original two models to show new morph model #3:
• hide #1,2 models or use the Models panel and unclick show checkbuttons.

• Play the morph:
• coordset #3 1,21

• Redisplay the bound galactose:
• show #1 model
• hide #1 ribbon

• Show residues near ligand
• coordset #3 0
• select zone ligand 5 #3 residues true
• show sel
• select clear

• Show protein closing around ligand
• coordset #3 20,0

• White background and silhouette edges:
• set bg white or press toolbar icon
• set silhouette true or press toolbar icon

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

• movie record supersample 3
  coordset #3 0,20
  wait 40
  coordset #3 20,0
  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...

6) Virtual reality view of binding site

Create a 360 degree 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 degree camera mode showing 0-360 degrees longitude and -90 to 90 degrees lattitude, top have 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 degree 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.