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.
- 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
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
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
- Open galactose binding protein in unbound state:
- open 2fw0
- Put both structures in view:
- view
or click toolbar icon
- Calculate an interpolation between two conformations:
- morph #1,2
- Use white background and silhouette edges:
- Command preset pub
or click toolbar icons
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
- 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.