Changes between Version 3 and Version 4 of COT

Timestamp:

Jun 25, 2009, 10:59:29 AM (17 years ago)

Author:

goddard

Comment:

--

COT

@@ -5 +5 @@
 
 don't include papers... they will go in the Chimera Software Dev project
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-2008/2009 report
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-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
-
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 2009/2010 report
@@ -365 +29 @@
 
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+[wiki:COT09 2008/2009 report]
+---------------------------------------------------------------------------