Movie Making in Chimera

Tom Goddard
May 5, 2009
UCSF Mission Bay Library

Goals

Scripts and PDB files used: movie_data.zip

Spin 360 degrees - The mother of molecular animations 

Open maltotriose binding protein and make it look good.

	File / Open -> 2gha-chain-A.pdb

	Presets / Interactive 1 (ribbons)

Spin and make movie.

	Favorites / Command-line

	turn y 3 120

	Tools / Utilities / Movie Recorder

	Record, turn y 3 120, Stop

	Output file Browse, Desktop/m1.mov, Make Movie

	double click m1.mov on desktop and play

	Note: default playback speed is 25 frames per second.



Cut out initial/final segments with no motion.

	movie record ; turn y 3 120 ; wait 120 ; movie stop

	movie encode output ~/Desktop/m2.mov

	Play movie m2.mov

Rock instead of spin to emphasize bound ligand.

	rock y

	freeze

	rock y 3 68		# 3 degree steps, 68 frames for one cycle

	rock x 3 68

	File / Open script m3.cmd to record movie

		movie record
		rock y 3 68
		wait
		rock x 3 68
		wait
		movie stop
		movie encode output ~/Desktop/m3.mov

	File / Open -> m3.cmd

	Play movie m3.mov

Improving the movie appearance.  Spin centered on the maltriose ligand.



	Select / Residue / MLR, then Actions / Set Pivot

	windowsize 640 480		# Larger window size

	set bg_color white		# white background

	Tools / Viewing Controls / Effects, silhouettes on

	Open script m4.cmd to record movie.

	Play movie m4.mov

Improve rendering quality.  Increase movie bitrate.

	Use "movie encode bitrate 10000" in script m5.cmd, default bitrate 2000 Kbits / sec.

	Movie file size will increase proportional to bitrate.

	Play movie m5.mov









Default bitrate 2000.
Bitrate 10000 Kbits/sec.



To avoid final frame of movie looking bad, add 10 stationary frames at end.

	Add "wait 10" command before "movie stop",  m6.cmd

	Play movie m6.mov

Reduce jagged edges.  Use supersampling.

	Use "movie record supersample 3" in script m7.cmd

	9 times slower recording movie.

	Play movie m7.mov









No supersampling.
Supersample 3 by 3.



Raytraced rendering to produce shadows.

	Use "movie record raytrace true" in script m8.cmd

	Very slow recording movie.  Time depends on scene complexity and window size.
	Make window size small and only show ligand as spheres for example.

	Play movie m8.mov

Volume data movie 

Movie showing sections of rat cortex from electron microscopy.

	File / Close session

	File / Open -> ratbrain.cmap

	Volume dialog, style solid, Features / Planes, One plane

	windowsize 892 772	# match volume data size

	Move volume dialog Plane slider.

	volume #0 planes z,0,100

	Open script r1.cmd to record movie.

	Play movie r1.mov

Command Documentation 

Two easy ways to access Chimera command documentation.  Use "help" command

	help volume

Or go to Chimera web site (google Chimera), click Command Index link at left.
Documentation for the movie command links to other useful commands.
Commands do not exist for all Chimera capabilities (for example, Morph Map).

Animation gallery at Chimera web site has example animations.

More Movie Examples

Morphing between atomic models. NMR ensemble of RNA stem loop that convinces ribosomes to translate viral RNA without methylguanosine mRNA cap.

Molecular dynamics trajectories. Beta hairpin of G protein with hydrogen bonds identified at each frame of trajectory.

Morphing between two maps. RNA polymerase in two conformations.

More examples from Chimera animation gallery.

Other Animation Software

Chimera makes only simple animations. Here is a movie made using Autodesk Maya commercial animation software with data exported from Chimera.

Clathrin cage assembly by Janet Iwasa, Harvard Medical School.

Start playing mid-way through.

Chimera Animations with Multiple Stages

Example Chimera movie with several stages. 

Movie mbp.mov made with script mbp.cmd.

How to add titling.

	Tools / Utilities / 2D Labels, click in graphics window and type text.
	Move label with mouse.

	Command version 2dlabel allows fading labels.
	(Dialog label ids are label2d_id_0, label2d_id_1, ...)

	2dlabel create MBPintro text "Binding maltotriose" xpos 0.3 ypos 0.92 color black

	2dlabel change MBPintro visibility hide frames 25
	(Chimera 1.4 bug makes fade abrupt after solid volume shown.  Restart.)

Making the maltotriose ligand fly.

	File / Close Session

	File / Open, 2gha-chain-A.pdb and 2ghb-chain-A.pdb

	Presets / Interactive 1 (ribbon)

	Select / Residue / MLR
	Select / Invert (selected models)
	Actions / Ribbon / hide
	Actions / Atom+Bond / hide
	
	Move models to lower left corner

	savepos p1

	Active models, turn off #1 with checkbutton below command-line.
	Move ligand to upper right with mouse and rotate.

	savepos p2

	reset p1 100

	Command script f1.cmd for flying ligand f1.mov.

Exercise: Morph Molecule

Use the morph conformations tool to show different configurations of the HIV packaging signal, RNA stem loop 1 (pdb 1m5l). 

	File / Close session

	File / Open, 1m5l.pdb

	Presets / Interactive 1 (ribbon)



	Tools / Structure Comparison / Morph Conformations

	Morph dialog, Add... button, drag mouse to select
	 all 15 models, press Add.
	Then choose first model, and press Add.
	This makes morph loop back to starting conformation.

	Morph dialog, set Action on Create to "hide conformations".

	Morph dialog, press Create.

	Actions / Color / by element

	MD Movie dialog will appear, press play button (triangle pointing right).

	MD Movie dialog, File / Record movie, /Users/.../Desktop/1m5l.mov, Record

	Command script 1m5l.cmd for RNA morph 1m5l.mov.