--------------------------------------------------------------------------- "Chimera Outreach and Training" subproject for CGL annual report reporting period is approximately June through May --------------------------------------------------------------------------- 2008/2009 report --------------------------------------------------------------------------- Jun 3, 2008 UCSF Library Course: Molecular Visualization with UCSF Chimera: Getting Started, 9-11am at the UCSF Mission Bay Campus. This session will go over the basics of molecular visualization and provide an introduction to how to use UCSF Chimera to load, visualize, and manipulate protein structures. Topics include: installing Chimera; Chimera menus and commands; fetching protein structures from ModBase and PDB; selections and actions; depictions; key tools: Side View, Model Panel, and the Selection Panel; and saving your work: sessions and images. Participants should have a basic understanding of protein structure. All participants will receive a CD with UCSF Chimera installers for Mac, PC, and Linux as well as example files and additional exercises. - Scooter Morris, Conrad Huang Jun 17, 2008 UCSF Library Course: Molecular Visualization with UCSF Chimera: Basic Tools, 9-11am at the UCSF Mission Bay Campus. This session will cover general structure visualization and analysis with Chimera. Topics include: identifying hydrogen bonds and contacts; measuring distances and angles, rotating bonds; viewing amino acid sidechain rotamers, "mutating" residues; displaying attributes such as B-factor and residue hydrophobicity; superimposing and comparing structures, morphing; viewing NMR ensembles and molecular dynamics trajectories. Participants should have an acquaintance with molecular graphics and protein structure, although expertise with Chimera is not required. Participants are encouraged to bring structures of interest (or note their Protein Data Bank IDs for retrieval in the lab) as "real-life" examples to supplement the exercises that will be provided. - Elaine Meng, Scooter Morris Jul 1, 2008 UCSF Library Course: Exploring Sequence-Structure Relationships with UCSF Chimera, 9-11am at the UCSF Mission Bay Campus. This session will cover working with protein sequence alignments together with 3D structures. Topics include: Web resources for protein family sequence alignments; sequence-structure association and crosstalk; calculating alignment conservation and displaying it on structures; using the alignment to match (superimpose) structures; matching structures without a pre-existing alignment; creating sequence alignments from multiple structure superpositions; customizing alignment appearance in Chimera; editing and saving. Participants should have at least a little experience with Chimera and a basic understanding of protein structure and sequence alignments. Participants are encouraged to bring data on systems of interest (structure IDs, and if available, corresponding sequence alignments) as "real-life" examples to supplement the exercises that will be provided. - Elaine Meng, Eric Pettersen Jul 15, 2008 UCSF Library Course: Working with EM and X-ray Density Maps in UCSF Chimera, 9-11am at the UCSF Mission Bay Campus. This session offers hands-on training for studying density maps, especially those from electron microscopy. You'll look at maps of phage K1E, a virus that infects E. coli, and learn to segment the protein coat from the packaged DNA genome, color to distinguish virus surface structures, morph to compare related viruses, and fit atomic models into the maps. The same techniques are applicable for crystallographic and tomographic density maps. Participants should have familiarity with Chimera. - Tom Goddard Jul 19, 2008 "Introduction to Molecular Visualization" tutorial at ISMB 2008 (16th Annual International Conference, Intelligent Systems for Molecular Biology, Toronto) http://www.iscb.org/ismb2008/tutorials.php 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. - Scooter Morris, Eric Pettersen Jul 22, 2008 "StructureViz: Cytoscape and Chimera" technology track demo at ISMB 2008 (16th Annual International Conference, Intelligent Systems for Molecular Biology, Toronto) http://www.iscb.org/cms_addon/conferences/ismb2008/techtrack.php - Scooter Morris Jul 29, 2008 UCSF Library Course: Publication-Quality Images and Movies with UCSF Chimera, 9-11am at the UCSF Mission Bay Campus. This session provides hands-on training for creating images and movies of molecular models and density maps for journal articles and presentations. You'll be introduced to the myriad of options to enhance your graphics: raytracing, depth cueing, supersampling, ribbon styles, silhouette edges, subdivision level, text labels, clipping and capping, transparent or colored backgrounds, fish eye views, presets, lighting, shininess, ambient occlusion, lenticular images, and movie transitions and encoding. You'll try these techniques on your own data (downloaded or brought on a flash drive or CD) or using example data we provide. Participants should have familiarity with Chimera. - Tom Goddard, Greg Couch Jul 31, 2008 30-minute demonstration of Cytoscape and Chimera to ~12 undergraduate students (from the organic chemistry class, University of San Francisco) - Scooter Morris, Elaine Meng Aug 5, 2008 UCSF Library Course: Customizing and tailoring UCSF Chimera, 9-11am at the UCSF Mission Bay Campus. This session will cover methods for customizing Chimera for specific tasks and projects. Topics include: writing command and demonstration scripts; accessing Chimera data structures using Python; adding per-frame actions for analyzing molecular dynamics; adding user-defined headers to sequence alignment displays; adding your own user interface elements to Chimera. Participants should have hands-on experience with Chimera. If there is a topic of particular interest, please mention it at the beginning of the session (or contact us beforehand) to ensure that we allot sufficient time to go into details. - Eric Pettersen, Conrad Huang Aug 19, 2008 UCSF Library Course: Exploring Protein Similarity Networks with Cytoscape, UCSF Chimera, and SFLD, 9-11am at the UCSF Mission Bay Campus. This session will cover the tools and methods that have been developed at UCSF to explore protein similarity networks. A protein similarity network is a network of nodes and edges where the nodes represent the protein and the edges represent some measure of the similarity between the proteins. These networks have been used to infer functional and evolutionary relationships between proteins and protein families. Session topics include: overview of protein similarity networks; using SFLDLoader to import protein similarity networks into Cytoscape; Cytoscape layouts suitable for protein similarity networks; exploring structural relationships with structureViz; creating your own protein similarity network; adding structural annotation to an existing protein similarity network. Participants should be familiar with Cytoscape and have some experience with molecular structure visualization. - Scooter Morris Nov 13, 2008 NCRR PI meeting, Bethesda, Maryland. Presentation of multiscale modeling capabilities with animations of rat brain data and Space Navigator use. - Tom Ferrin Dec 2008 Chimera used to create image for RBVI holiday card: 20S Proteasome. - Tom Goddard, Scooter Morris Dec 11, 2008 Demonstration for donors to the UCSF School of Pharmacy: visualization of the 8-segment RNA genome of influenza virus in electron microscope tomography data using special-purpose hardware: LCD stereo glasses, Space Navigator 6-degree-of-freedom input device, and Phantom force feedback input device for marker placement. - Tom Goddard Dec 12, 2008 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 Jan 14, 2009 Chimera demonstrations for high school students participating in the Science and Education Partnership. Two half-hour demonstrations to Lincoln High School students and instructors (~18 total): viewing a nanomachine and the enzyme mevalonate kinase in stereo. - Tom Goddard Jan 23, 2009 Talk on electron tomography for Automated Molecular Imaging forum, Scripps Research Institute. ~60 attendees. - Tom Goddard Feb 1, 2009 Talk on electron tomography entitled "Interactive Visualization of Spikes, Pores and Cages" at Asia-Pacific Congress on Electron Tomography, Brisbane, Australia. ~150 attendees. http://homepage.mac.com/marshbj/APCET/ - Tom Goddard Feb 28, 2009 Presentation on current AMBER-related Chimera features and plans for further development at the AMBER developers' meeting (Feb 28-Mar 1), St. Simons Island, Georgia. ~30 attendees. - Eric Pettersen Mar 1-3, 2009 Biophysical Society 2009, Boston: RBVI staff will be giving several presentations at the NIH NCRR exhibitor booth. http://www.cgl.ucsf.edu/events/BPS2009/ - Scooter Morris, Tom Goddard Mar 31, 2009 UCSF Library Course: Molecular Visualization with UCSF Chimera: Getting Started 10am-noon at the UCSF Mission Bay Campus. http://www.library.ucsf.edu/help/classes This session will go over the basics of molecular visualization and provide an introduction to how to use UCSF Chimera to load, visualize, and manipulate protein structures. Topics include: installing Chimera; Chimera menus and commands; fetching protein structures from ModBase and PDB; selections and actions; depictions; key tools: Side View, Model Panel, and the Selection Panel; and saving your work: sessions and images. Participants should have a basic understanding of protein structure. All participants will receive a CD with UCSF Chimera installers for Mac, PC, and Linux as well as example files and additional exercises. - Scooter Morris, Conrad Huang Apr 7, 2009 UCSF Library Course: Analyzing and Comparing Structures with UCSF Chimera 10am-noon at the UCSF Mission Bay Campus. This session will cover general structure visualization and analysis with Chimera. Topics include: identifying hydrogen bonds and contacts; measuring distances and angles, rotating bonds; viewing amino acid sidechain rotamers, "mutating" residues; displaying attributes such as B-factor and residue hydrophobicity; superimposing and comparing structures, morphing; viewing NMR ensembles and molecular dynamics trajectories. Participants should have some knowledge of protein structure and molecular graphics, but expertise with Chimera is not required. Participants are encouraged to bring structures of interest (or note their Protein Data Bank IDs for retrieval in the lab) as "real-life" examples to supplement the provided exercises. - Elaine Meng Apr 14, 2009 UCSF Library Course: Exploring Sequence-Structure Relationships with UCSF Chimera 10am-noon at the UCSF Mission Bay Campus. This session will cover working with protein sequence alignments together with 3D structures. Topics include: customizing alignment appearance in Chimera; sequence-structure association and crosstalk; calculating sequence conservation and displaying it on structures; matching (superimposing) structures using an alignment; comparing structures of the same protein or different but related proteins; creating sequence alignments in Chimera; other sources of sequence alignments. Participants should have some experience using Chimera and a basic understanding of protein structure and sequence alignments. Participants are encouraged to bring data on systems of interest (structure IDs, and if available, corresponding sequence alignments) as "real-life" examples to supplement the provided exercises. - Elaine Meng, Eric Pettersen Apr 21, 2009 UCSF Library Course: Electron Microscope Tomography in UCSF Chimera 10am-noon at the UCSF Mission Bay Campus. This course provides hands-on training exploring electron tomography maps. You'll learn to trace membranes, mask and extract structures, filter data, and fit models in cellular tomograms containing microtubules, nuclear pores, vesicles and assorted subcellular structures. Chimera map capabilities are also useful for single-particle EM reconstructions and x-ray crystallography maps and researchers studying those data types may benefit from this course. Participants should have familiarity with Chimera. - Tom Goddard Apr 28, 2009 UCSF Library Course: Publication-Quality Images with UCSF Chimera 10am-noon at the UCSF Mission Bay Campus. This session provides hands-on training for creating images for journal articles and presentations. You will be introduced to the myriad of options to enhance your graphics: presets, depth cueing, transparency, silhouette edges, lighting, shininess, text labels, clipping and capping, color choices, raytracing, supersampling, subdivision quality, transparent backgrounds for image compositing, ribbon styles, stereo pairs, fish eye views, ambient occlusion, and lenticular images. Then you'll try some of these techniques on your own data (downloaded or brought on a flash drive or CD) or with example data we provide. Participants should have familiarity with Chimera. - Greg Couch May 5, 2009 UCSF Library Course: Movie Making with UCSF Chimera 10am-noon at the UCSF Mission Bay Campus. This course provides hands-on training creating movies of molecular models for journal articles and presentations. You'll create an animation showing a ligand binding to a receptor with morphing between unbound and bound states. Titling, movie encoding, animation commands, and effects (edging highlighting, shininess, smoothing) will be covered. Participants should have familiarity with Chimera. - Tom Goddard May 12, 2009 UCSF Library Course: Customizing and Tailoring UCSF Chimera 10am-noon at the UCSF Mission Bay Campus. This session will cover methods for customizing Chimera for specific tasks and projects, writing command scripts, and programming Chimera in Python. Other topics will be covered based on attendees interests. Please send mail to chimera-dev-classcgl.ucsf.edu if you would like to see a specific topic covered in depth. Possible topics include (but are not limited to): per-frame scripting of molecular dynamics trajectories; using the Demo Editor; adding user-defined headers to sequence alignments; writing Chimera extensions or commands. Participants should have hands-on experience with Chimera. - Eric Pettersen, Conrad Huang --------------------------------------------------------------------------- [wiki:COT08 2007/2008 report] ---------------------------------------------------------------------------