Changes between Initial Version and Version 1 of COT09

Timestamp:

Jun 25, 2009, 10:57:35 AM (17 years ago)

Author:

goddard

Comment:

--

COT09

@@ +1 @@
+---------------------------------------------------------------------------
+"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)
+  - 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.
+ - 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.  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.
+ - 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
+