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don't include papers... they will go in the Chimera Software Dev project

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"Chimera Outreach and Training" subproject for CGL annual report

activities Jun 1, 2007 - May 31, 2008

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May 16, 2007

Chimera training held at UCSF for Richard Newman who creates visualizations for the Electron Microscopy Data Bank run by the European Bioinformatics Institute.

• Tom Goddard

Jun 8, 2007

Chimera Release Party - Genentech Hall, UCSF (>100 attendees) A few days before the event, flyers were posted in Genentech Hall and other buildings at the Mission Bay Campus. Over 100 people attended to learn about Chimera and to enjoy pizza and other refreshments. Chimera was demonstrated on Mac and Windows computers, both connected to projectors. Handout materials summarized reasons to try Chimera as a new user, or to upgrade to the new version from prior versions. Also handed out were red-cyan stereo glasses, to work with the anaglyph display option, and a short survey about experiences with Chimera and other visualization software. 106 surveys were retrieved.

• all Chimera team members

Jul 16, 2007

"What's New in Chimera presentation" - Babbitt group, UCSF (~15 attendees) Advanced features were shown using live demonstrations accompanied by an HTML outline and linked pages. The emphasis was on recently added or improved features, including: raytracing, presets, red-cyan stereo, movie recording options, morphing, clash detection, assignment of charges and other parameters, minimization, rotamer libraries, and sequence alignment editing. The web materials were added to the Babbitt group wiki (private).

• Elaine Meng and Eric Pettersen

Aug 13, 2007

"Introduction to Molecular Visualization" Tutorial at the Computational Systems Bioinformatics (CSB) conference - University of California, San Diego (8 attendees). Abstract:

Projects such as Structural Genomics are providing increasing numbers

of experimental protein and protein-complex structures. Furthermore, increasing numbers of theoretical models are being predicted from primary sequence. Biologists have an increasing need to understand and communicate the structures, functions and relationships between these protein and protein-complex structures. As a result, molecular visualization is becoming an important tool for the presentation and communication of the results of biological experiments and research. This tutorial will provide a basic foundation for the understanding of molecular structures through use of visualization tools.

Attendees will learn the basics of molecular visualization and will be

provided an overview of available tools and techniques for visualization, analysis and modeling of protein structure. To make these concepts more concrete, attendees will be shown the academic program UCSF Chimera in more detail, and receive instruction in its features and use. The field of structural biology is still changing, and new techniques are continually being developed. Attendees will be shown how they can add new analysis techniques and their own data to the visualization.

• Scooter Morris and Conrad Huang

Oct 22, 2007

Two 20-min presentations on work done at the RBVI (each to 8 students) as part of an annual colloquium sponsored by the NSF's Alliances for Graduate Education and the Professoriate (AGEP). An example research scenario was illustrated with live demonstrations of Cytoscape and Chimera. AGEP's mission is to increase the number of underrepresented minority students who pursue graduate degrees and careers in the sciences and academia. The Colloquium is a two-day outreach and informational event that brings underrepresented undergraduate students to UCSF to learn about our graduate programs. This year's focus was on programs in Biophysics, Bioinformatics, and Systems Biology.

• Scooter Morris and Elaine Meng

Nov 3, 2007

UCSF School of Pharmacy Homecoming lab tours - presentations to groups of 14 and ~30 alumni on projects of the RBVI, including demonstrations of Cytoscape and Chimera.

• Scooter Morris

Nov 14, 2007

30-min demo "Interactive Map Visualization with UCSF Chimera" at the NRAMM (National Resource for Automated Molecular Microscopy) Workshop on advanced topics in EM structure determination, November 10-16, 2007, The Scripps Research Institute, La Jolla, CA. ​http://nramm.scripps.edu/seminars/2007/cryoem/

• Tom Goddard

December 6, 2007

Chimera Release Party and RBVI Open House (2-5 pm in Genentech Hall N453, UCSF Mission Bay) for local researchers and students to meet the Chimera developers, see demonstrations and discuss features, tour the RBVI facilities, and share refreshments.

• Chimera team

December 17, 2007

Chimera demonstration for Greg Farrington, executive director of the California Academy of Sciences, and Bruce Alberts, professor of biochemistry and biophysics, UCSF.

• Tom Goddard

Feb 3-5, 2008

Chimera demonstrations at the NCRR booth, 2008 Biophysical Society Annual Meeting, Long Beach, CA. Summaries:

Title: Introduction to the UCSF Chimera molecular modeling package Presenter: Scooter Morris Abstract: UCSF Chimera is a program for interactive molecular graphics and modeling. It provides standard graphics features as well as more unique, domain-specific tools; the menu and command-line interfaces provide a rich and overlapping set of functionality. The Introduction to Chimera shows frequently used coloring and display options, including molecular representations such as ribbons, "pipes and planks," surfaces, and abstract renderings of nucleotides. Other general features shown are distance measurements, bond angle rotations, H-bond identification, and display of the corresponding amino acid and/or nucleotide sequences. Attributes such as B-factors and hydrophobicities can be rendered visually with colors, atomic radii, and "worm" thickness. Chimera includes detailed user documentation and is available for Windows, Linux, Mac OS X (with X11), IRIX, and Tru64 Unix. Chimera is free for academic, government, and non-profit use and can be downloaded from ​http://www.cgl.ucsf.edu/chimera

Title: New Features in UCSF Chimera Presenter: Elaine Meng, Eric Pettersen Abstract: UCSF Chimera is an interactive molecular graphics program with a wide variety of features. Applications include structure analysis (hydrogen bonding, contacts, clashes), structure superposition and comparison, ensemble analysis (trajectory playback, ensemble clustering), analysis in the context of other types of data (sequence alignments, density maps), and making high-quality images and movies.

Recently added features include display and incorporation of amino acid sidechain rotamers from backbone-dependent and -independent libraries, creation of "morph trajectories" between different conformations of a protein or even different proteins, and generating shadowed images with POV-Ray, which is embedded in Chimera. We will demonstrate these features as well as other features (whether new or not) upon request.

Title: Visualizing 3-D Electron Microscopy Data with UCSF Chimera Presenter: Thomas Goddard Abstract: I'll demonstrate some new capabilities of the UCSF Chimera visualization program ( www.cgl.ucsf.edu/chimera) including tracing surfaces of intracellular membranes or virus layers in electron microscopy density maps, extracting density within surfaces, slicing tomography data at arbitrary angles to show nuclear pores, and displaying data cross-sections as topographic relief surfaces.

UCSF Chimera is an interactive molecular graphics program for analysis of proteins, nucleic acids, volumetric and sequence data. and for creating publication images. The density map display and analysis capabilities are being developed for studying single particle reconstructions and EM tomography.

Feb 6, 2008

Chimera presentation for discussion session on tomographic software, National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, CA.

• Tom Goddard

Apr 4, 2008

Chimera demonstration showing electron microscopy data and crowded cellular environments to three high school visitors.

• Tom Goddard

Apr 14, 2008

Chimera demonstration for post-doc and programmer from the National Center for X-ray Tomography (at LBNL), showing stereo visualization, force feedback and 3D input devices, head tracking, and lenticular images.

• Tom Goddard

Apr 17, 2008

Demonstration of Chimera to a dozen students from Lincoln High School.

• Tom Goddard

Apr 24, 2008

Kids at UCSF Day. Two 90-minute sessions with up to 10 elementary- and middle-school-age children, on the theme: "What causes colds and flu? See, hold and feel these bugs using 3 dimensional computer virtual reality." Interactive molecular graphics with Chimera and paper models of viral capsids will be used.

• Tom Goddard, Elaine Meng

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