Chimera Demonstrations, Talks and Posters

ChimeraX medical imaging in VR features added for NIAID. February 25, 2019.

Color protein surface by NMR chemical shift perturbations with Chimera 1.13 with notes on pitfalls. November 28, 2018.

VR on Windows laptops using ChimeraX. November 20, 2018.

Virtual Reality on macOS for using ChimeraX. November 15, 2018.

How to set up virtual reality on linux for using ChimeraX. October 26, 2018.

Opioid drug binding ChimeraX virtual reality demo. October 10, 2018.

New UCSF VR web site. June 15, 2018.

ChimeraX virtual reality example mutating a residue. June 11, 2018.

Comparing bound ligands with Chimera 1.12. December 7, 2017.

Fit HSP90 into negative-stain EM with Chimera 1.12. December 6, 2017.

Color protein surface by NMR chemical shift perturbations with Chimera 1.12. November 29, 2017.

Mark protrusions on cells in ChimeraX. November 9, 2017.

Virtual reality example data showing molecular systems with ChimeraX. November 2, 2017.

Cell motion light microscopy movies of crawling neutrophils from Lillian Fritz-Layin and Dyche Mullins, data from actin protrusions article. July 19, 2017.

How to place markers on 3d image time series using Chimera. May 26, 2017.

Place actin filament templates on hair cell stereocilium tomography. May 24, 2017.

Working with 3d image time series in ChimeraX. April 21, 2017.

Movie making for cryoEM with ChimeraX tutorial for SBGrid. April 11, 2017.

Ribosome antibiotic ChimeraX virtual reality demonstration, for Byer's Lecture reception. January 27, 2017.

ChimeraX virtual reality how-to guide for using HTC Vive and Oculus Rift headsets and recording VR movies. December 16, 2016.

ChimeraX integrative hybrid model site visit demonstration. November 8, 2016.

ChimeraX features presentation to advisory committee. March 21, 2016.

Molecular Lipophilicity Potential and comparisons with a few related methods. Aug-Sep 2016.

Chimera 2 features presentation to advisory committee. March 25, 2015.

Hands-on kilobot demo for prospective UCSF students. February 6, 2015.

Kilobot, T-cell and cancer exhibit for Byer's lecture. January 29, 2015.

Ebola glycoprotein visualization for Baylor College of Medicine class "Computational Mathematics for Biomedical Scientists". September 25, 2014.

Ambient occlusion lighting tests. July 8, 2014.

Drawing outlines of epitopes on surfaces. May 2, 2014.

Oculus Rift molecular visualization tech note. March 11, 2014.

Using the Structure-Function Linkage Database (SFLD) and Chimera for enzyme functional annotation (2014 update of demo from November 2011).

Group meeting presentation of brain planetarium video, neurodome project, oculus rift stereo goggles. February 3, 2014.

Difference map coloring. January 3, 2014.

Building a molecular filament model. January 3, 2014.

Analytic solvent accessible surface area calculation. November 4, 2013.

Evaluation of molecular surfacing methods, including distance grid solvent excluded surfaces, MSMS surfaces, Gaussian surfaces, sum of balls surfaces, LSMS surfaces, PyMol surfaces. October 14, 2013.

mmCIF file format issues presented at the Workshop on the PDBx/mmCIF data exchange format, October 22, 2013.

Snake venom and nicotinic acetycholine receptor analysis demonstration for Baylor College of Medicine graduate students. September 19, 2013.

Bent microtubule geometric model. August 2, 2013.

Multiscale brain demo showing light microscopy of whole human brain, traced neurons, rat cortex electron microscopy, neural synapse tomography, acetylcholine receptor synapse ion channel, and snake neurotoxin. COSMOS science demo. July 25, 2013.

Big Brain high resolution human brain imaging shown in Chimera. July 12, 2013.

Water and drugs examples of simple molecular structures for Oakland Dewey High School students. March 8, 2013.

Poster presentation to NIH 2013 P41 meeting, showing animation capabilities and web services. Associated storyboard.

Protein sculpture web application presented at RBVI group meeting Feb 4, 2013.

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.