Movie Making for cryoEM using ChimeraX

Tom Goddard
SBGrid Webinar
April 11, 2017

What is ChimeraX?

ChimeraX is the next generation version of Chimera.
It will replace Chimera in a couple years, but has new features that may be usful to you now, e.g. ambient occlusion lighting.
Nightly builds are on the web site. SBGrid also has it, but will be less frequently updated on SBGrid.

Today's topics

Movie making for cryoEM structures.

Ambient occlusion lighting.
Morph atomic structure of virus.
Show fit of each residue in cryoEM density.
Cellphone virtual reality 360 degree movies.

Ambient occlusion lighting

Rotavirus EMD 5199, 3.8 Angstrom, 1 octant of map, 500³ grid points.
open 5199 from emdb
Adjust contour level using vertical bar on histogram. Adjust step from 2 to 1 (full resolution).
volume #1 level 0.1 step 1
Ambient shadows make indentations dark.
light soft
Compare to simple lighting and single shadow.
light simple
light shadow true
Fit atomic model PDB 4v7q, ambient lighting helps depth perception.
open 4v7q
Color zone to color map to match atomic model.
color zone #1 near #2 distance 5
Hide dust.
surface dust #1 size 5

Morphing

Deformed wing virus, honey bee pathogen, colony collapse disorder.

cryoEM virus capsid structure 5mv5 (3.1 A, EMDB 3574)
open 5mv5
x-ray structure 5g52 (3.8 A)
open 5g52
Align structures with matchmaker
matchmaker #2 to #1
Morph to show large domain motion.
morph #1,2
color #3 bychain
coordset #3 1,21
Different conformations of surface domain of VP3, moves 39 A and rotates 145 degrees.
Record a movie. Movie.
movie record ; coord #3 1,21 ; wait 25 ; movie encode ~/Desktop/dwv.mp4

Morph full virus capsid

Show morph of full virus capsid.
sym #3 i,222
Hide ribbon, show atoms as spheres, turn on ambient shadows (use toolbar icons instead of commands).
hide ribbon
show atoms
style sphere
light full
Show morph. Slow with ambient shadows (1 second per frame), so use simple lighting.
light simple
coordset #3 1,21
Record a movie with full lighting. Movie.
light full
movie record ; coord #3 1,21 ; wait 25 ; movie encode ~/Desktop/dwv.mp4

Show residues fit in cryoEM density

Close previous structures.
close
Open atomic model and EMDB map.
open 5mv5
open 3574 from emdb
Start residue fit display for chain A.
resfit #1/A map #2
Use slider and play buttons to display each residue in sequence.
Record a movie. Press record button then stop button to make resfit.mp4 on desktop.

Virtual reality 360 degree images and movies

Immersive view from inside deformed wing virus 5-fold symmetry axis pore. 360 degree stereoscopic molecular scene can be viewed using a cellphone and a virtual reality headset.

Record image or movie using camera mode 360tb.
camera 360tb
Top have is left eye 360 degree image, bottom is right eye 360 degree image.
Use a square window size.
windowsize 600 600
Record high resolution image, e.g. 4k by 4k. Full 4k image.
save ~/Desktop/dwv360.png width 4096 height 4096
Use cellphone VR viewer application such as Mobile VR Station on iPhone with a VR headset to view the scene. (Useful to turn off auto-brightness on cellphone.)