Demonstration of termite gut segmentation for the Northern California Society for Microscopy, November 15, 2012.
Test of smoothing boundaries of masked density maps, September 2012.
How to create map and molecule morph movies. Bay Area cryoEM meeting, Santa Cruz, August 2012.
Tutorials on segmenting HIV electron tomography and how to make high quality images and more presented at the National University of Singapore cryoEM workshop, July 12, 2012.
Demonstration showing HIV core architecture. November 2011.
Building a tetrahedral model of alpha crystallin in an electron microscopy map. Demonstrates combined use of many Chimera capabilities. Nov 17, 2011.
Fitting methods demonstration applied to alpha crystallin for 3D EM Gordon Conference, June 27, 2011. Long version.
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. April 7, 2011.
EMAN workshop tutorial fitting Rous sarcoma virus and comparison to HIV (video and data files). March 15, 2011.
Termite gut bacteria poster and web page showing segmentation and measurement methods applied to a focused ion beam scanning electron microscopy (FIBSEM) density map. October 9, 2010.
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. Group meeting. March 29, 2010.
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. February 26, 2010.
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.
Publication-Quality Images course notes from April 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.
Chimera surface rendering advances at group meeting, October 2008.
Volume display demonstration showing x-ray and EM maps, July 2008 Chimera course.
Tutorials used in hands-on Chimera courses (2008).
Movie making tutorial (2008).
Volume data analysis exercices (2008). Coloring using electrostatic potential, viewing crystal difference maps, solvent occupancy map, morphing between maps, erasing part of a map, tracing surfaces in tomograms.
Paper virus models from UCSF Kid's Day (2008).
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. Group meeting, March 2008.
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.
Crystal contacts of cowpea mosaic virus (2006).
Experimental features not yet included in the Chimera distribution (2006).
Guide to volume data display (2006).
Immune T-cell and microtubule demonstration notes. Demonstration at workshop on Visualization Tools for Cellular Complexity at Max Planck Institute for Biochemistry (2006).
Tomography and light microscopy of cells. Talk given at workshop on Visualization Tools for Cellular Complexity at Max Planck Institute for Biochemistry (2006).
Progress and plans for analyzing large assemblies. Prepared for NCRR site visit to renew Chimera funding (2006).
Placing markers on maps for analysis and modeling. Talk given at the Workshop on Multiscale Biological Imaging, Data Mining and Informatics (2006).
EM Databank Gallery (2005).
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). Shows ribosome, virus, and GroEL visualizations.
Tutorials for density map display, and exploring large complexes (2005).
Visualization of virus capsids. (2004)
Chimera Poster (2002) showing
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.