Demonstrates combined use of many Chimera capabilities. Fitting methods demonstration applied to alpha crystallin for 3D EM Gordon Conference, June 27, 2011. HIV capsid visualization created for Mo' MAGIC high school students, June 23, 2011. Chimera web log example fitting Rous sarcoma virus capsid protein into an electron microscopy map and comparing HIV capsid pentamers.
This is a hand mock-up of a proposed capability to automatically log Chimera analysis in HTML format including thumbnail images, numeric results and links to sessions, data files, movies, WegGL rotatable models and more. EMAN workshop tutorial fitting Rous sarcoma virus and comparison to HIV (video and data files). Termite gut bacteria poster and web page showing segmentation and measurement methods applied to a focused ion beam scanning electron microscopy (FIBSEM) density map. DNA visualization demonstration showing chromosomes (light and electron microscopy), molecular models, nucleosomes and chromatin. Presented to Celsius and Beyond summer camp students, June 9, 2010. V3D software for volume visualization and neuron tracing. Animations By and For the Common Researcher talk at Molecular Animation Workshop hosted by RBVI surveys movies included in Science articles in 2009 and problems limiting use of movies. Segger demonstration segmenting EM maps and fitting molecular models of groel and bacteriophage lambda presented at the AMI (Automated Molecular Imaging) Forum seminar series at Scripps, February 11, 2010.
HIV spike integrative data analysis demonstration for RBVI advisory committee meeting, November 2009. EM fitting one day training, HIV spikes and ParM filaments, from EMBO practical course, October 2009. Virus visualization demonstration for high school teachers arranged by UCSF Science and Health Education Partnership, May 2009. Movie making course, UCSF Mission Bay Library, May 2009. Examining nuclear pores in cellular tomography shown at Asia-Pacific Congress on Electron Tomography, February 2009 and at AMI Forum, January 2009. Visualizing mevalonate kinase shown to students from Lincoln High School SMART team, January 2009. GPU computing overview at group meeting, December 2008. Quaternary structure visualization at group meeting, November 2008. Volume display demonstration showing x-ray and EM maps, July 2008 Chimera course. Coloring using electrostatic potential, viewing crystal difference maps, solvent occupancy map, morphing between maps, erasing part of a map, tracing surfaces in tomograms. Recent advances: influenza tomography, space navigator, unified surface model, surface tracing, geometric shapes, fitting with simulated maps, angle-dependent transparency, thick surfaces, intertia axes of molecule. Influenza RNA segmentation from tomography data demonstrated for Jason Lanman and Jack Johnson, February 2008. X-ray tomography pombe cell segmentation demonstration, National Center for X-ray Tomography, February 2008. Experimental features not yet included in the Chimera distribution (2006). Demonstration at workshop on Visualization Tools for Cellular Complexity at Max Planck Institute for Biochemistry (2006). Talk given at workshop on Visualization Tools for Cellular Complexity at Max Planck Institute for Biochemistry (2006). Prepared for NCRR site visit to renew Chimera funding (2006). Talk given at the Workshop on Multiscale Biological Imaging, Data Mining and Informatics (2006). Demonstration showing myosin thick filament density map display and fitting given at Automated Molecular Imaging Forum, Scripps (2005). Tubulin showing electrostatic potential, crystallographic density map, and fitting model to EM density map. Presented at Chimera workshop at UCSF, November 2005. Thermosome model used to illustrate display of large multimeric systems at various resolutions.
Presented at Chimera workshop at UCSF, November 2005. Comparison of virus capsid shapes (2005) to surfaces obtained by linearly interpolating between an icosahedron and a sphere. Large biomolecular complexes workshop presentation (2005). Tutorials for density map display, and exploring large complexes (2005). Chromosome and virus visualization and modeling of electron microscope data using Volume Viewer, Volume Path Tracer, and Scale Bar extensions, Multiple sequence alignments and structures using the MultAlign Viewer extension, Screening of ligands docked to a receptor using the ViewDock extension. Talk on multi-scale modeling of viruses and chromosomes (2002). Visualizing volume data (2001) including x-ray and electron microscope density maps, electrostatic potentials, solvent occupancy maps, and multi-channel light microscope volumes. Chromosome structure analysis (2001) using electron and light microscopy from John Sedat's lab at UCSF. Virus structure analysis (2001) using electron microscope data from Wah Chiu's lab at Baylor College of Medicine. General structure analysis capabilities (1999) including display of mobility, ensembles, superpositions, residue properties, chemical groups, and addition of hydrogen atoms.
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