May 5, 2009
UCSF Mission Bay Library
Scripts and PDB files used: movie_data.zip
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.|
|No supersampling.||Supersample 3 by 3.|
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
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.
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.
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.
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.
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.