RBVI Workshops and Training Opportunities

Molecular Visualization with UCSF Chimera: Getting Started

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 Tuesday March 31, 2009 10am-12pm Mission Bay Community Center Library
Register for this course Analyzing and Comparing Structures with UCSF Chimera

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 & Scooter Morris Tuesday April 7, 2009 10am-12pm Mission Bay Community Center Library
Course materials Exploring Sequence-Structure Relationships with UCSF Chimera

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 Tuesday April 14, 2009 10am-12pm Mission Bay Community Center Library
Course materials Electron Microscope Tomography in UCSF Chimera

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 Tuesday April 21, 2009 10am-12pm Mission Bay Community Center Library
Course materials Publication-Quality Images with UCSF Chimera

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 Tuesday April 28, 2009 10am-12pm Mission Bay Community Center Library
Course materials Movie Making with UCSF Chimera

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 Tuesday May 5, 2009 10am-12pm Mission Bay Community Center Library
Course materials Customizing and Tailoring UCSF Chimera

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 Tuesday May 12, 2009 10am-12pm Mission Bay Community Center Library
Register for this course

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