Nuclear pores. January 23, 2009. flypores.mov (9 Mb)

Fly-by of 3 nuclear pores in a human T-cell seen in electron tomography using the fly command to smoothly transition between 4 saved view points. The fly command was added to Chimera 1.4 in January 2009.

Rat brain electron microscopy. November 13, 2008. rb.mov (25 Mb) rb.avi (25 Mb)

Shows 50 x 50 x 100 micron volume of rat cortex imaged by serial block-face scanning electron microscopy (details). Illustrates the challenge of segmenting neural connections.

Ligand binding and conformational change. July 28, 2008. mbp.mov (15 Mb)

Shows maltotriose binding protein (2gha) binding site, hydrogen bonds, nearby aromatic residues, and conformational change between bound and unbound states. A Chimera 1.4 command script mbp.cmd to make this movie is given in the 2009 movie making tutorial.

Flexibility of an NMR ensemble. June 23, 2008. 1r7w.mov (12 Mb)

Shows morphing between the 20 conformations of an NMR ensemble of a stem loop RNA (1r7w) that allow ribosomes to translate viral mRNA without the normally required methylguanosine mRNA cap.

Combinatorial scanning of human growth hormone. November 22, 2006. 3hhr-scan.mov (33 Mb)

Illustrates results from quantitative scanning mutagenesis of human growth hormone (hGH) to probe the hormone-receptor binding interface, described in Pal et al., J Biol Chem 281:22378 (2006). The movie was created with the Chimera command script 3hhr-scan.com (after removing ## from movie-recording commands), which in turn opens the file of scanning results 3hhr-scan.txt.

Sliced virus density map. October 5, 2006. em_1ynv_cut.mov (18 Mb)

Electron microscopy reconstruction of sulfolobus turretted icosahedral virus sliced perpendicular to a 5-fold symmetry axis. Low, medium and high density are shown in red, white and blue on the cut surface. The density map is VIPERdb 1ynv.

Traced chromosome arms. August 24, 2006. arms.mov (7 Mb)

Traced chromosome arms during Drosophila cell division. The chromatin was labeled with a histone-GFP fusion protein. The time between frames is 10 seconds. Data courtesy of Yuri Strukov.

Cell division. August 4, 2006. mitosis.mov (10 Mb)

3d optical miscroscopy time series showing dividing cells. This is an early, 2 hour old, Drosophila melanogaster embryo, in which chromatin is labeled with histone-GFP fusion protein. Frames were taken every 10 seconds. Thanks to Yuri Strukov for providing the data.

Myosin thick filament analysis. June 16, 2006. myomovie.mov (30 Mb)

Shows symmetry, fitting, and segmenting a myosin thick filament density map. Thanks to John Woodhead and Roger Craig for providing the map.

Actin filament nucleation. April 24, 2006. spire.mov (6 Mb)

Actin filament nucleated by Spir protein. This animation was created by Janet Iwasa based on work done by Margot Quinlan. It was made in Macromedia Flash using an actin monomer model exported from Chimera. More of Janet's animations and illustrations are at www.onemicron.com.

Myosin thick filament. February 17, 2006. myosin_slabs.mov (20 Mb)

Cross-section slabs of a myosin thick filament cryo-EM density map. The map comes from John Woodhead and Roger Craig, and is described in Nature. 2005 Aug 25;436(7054):1195-9.

Satellite Tobacco Mosaic Virus Genome. February 1, 2006. stmv-rna.mov (7 Mb).

Organization of the satellite tobacco mosaic virus genome. Single strand RNA, 1058 nucleotides, depicted as a tube with A, C, G, U shown in red, yellow, green, and blue.

Engrailed Homeodomain. January 20, 2006. enh.mov (3 Mb).

Folding of the engrailed homeodomain, PDB 1enh. The trajectory was created by Christophe Guilbert using the flexible docking program MORDOR.

Orthoreovirus. January 5, 2006. reovirus.mov (12 Mb).

Successive layers of orthoreovirus capsid fly away radially. The original version of this movie was created by Xing Zhang in Tim Baker's lab using other software. The PDB model is 2cse.

Beta hairpin. November 30, 2005. hairpin.mov (40 Mb).

Simulation of the C-terminal beta hairpin from protein G using AMBER shows water occupancy and hydrogen bonds between the hairpin and water molecules. Data provided by John Chodera. More details appear in the Chimera image gallery entry.

Myosin thick filament. October 5, 2005. myosin.mov (8 Mb).

Shows 12 pairs of myosin heads arranged helically as in a thick filament. One pair is being moved around interactively and the others move to preserve the helical symmetry. Automatically maintaining symmetry is useful for interactive fitting of molecules into symmetric density maps. The PDB model is 1i84.

Follicle stimulating hormone. October 3, 2005. hrc_demo.mov (43 Mb).

Overview of follicle stimulating hormone and its receptor. This movie was captured by playing the Hormone-Receptor Complex demonstration which is included with Chimera (under menu Tools / Demos). The PDB model is 1xwd.

Rice Dwarf Virus. September 23, 2005. ricedwarf.mov (6 Mb).

Concentric shells of a rice dwarf virus density map are shown. Low densities are shown in red, high in blue. A shell that is interpolated in shape between an icosahedron and a sphere is used. The shell radius is shown in angstroms in the lower left corner. The data is EM Databank entry 1060.