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= Ideas and discussions for the RBVI 2011 Site Visit =

== Scenarios ==
=== Scenario 1 ===
 * SFLD/Cytoscape/Chimera
 * (Scenario #1 from 2009 Advisory Committee mtg: [https://plato.cgl.ucsf.edu/trac/SFLD/wiki/RBVIAdvisoryCommitteeMeeting#no1])

=== Scenario 2 ===
 * Chimera/Volume Tools/Cytoscape(?)
 * (Scenario #2 from 2009 Advisory Committee mtg: [https://plato.cgl.ucsf.edu/trac/chimera/wiki/HIVspikes])

== Ideas of what to show ==
=== TR&D 1 ===
 * BLAST service
 * Modeller interface
 * multiple alignment Conservation header (sequence conservation, AL2CO options include entropy, variability, etc.)
 * multiple alignment RMSD header (spatial conservation of associated superimposed structures)
 * render by attribute (could be attribute from MAV header or other such as bfactor or Modeller error profile)
 * UniProt annotations on sequence either from direct UniProt fetch of sequence or using PDB/UniProt Info tool
 ** if useful for system... good for showing relationship of gp120 core constructs in which loops had been replaced with stubs to the full-length sequence (unfortunately PDB SIFTS service has a data problem with 1GC1 but 1GM9 is nearly identical and could be used instead)

=== TR&D 2 ===
 * Building a "composite model" and linking molecules, maps and sequences of components.
 * Chimera analysis web log.  Would be cool to demo WebGL embedded in Chimera log then shown on a smart phone or tablet as a way to facilitate hallway/lecture-hall/lunch collaborative work.

 ==== Biological Systems ====

 Alpha Crystallin
 * [http://plato.cgl.ucsf.edu/chimera/data/3dem-june2011/fitdemo_long.html Alpha Crystallin] - Already prepared multifaceted demo including BLAST, homology modeling, crystal unit cell, EM fitting, and SAXS, for Gordon conf but cut due to time limits.  Connected to heart disease, cataracts and amyloid aggregation diseases.
 * Clathrin cage tomography from Yifan Cheng.  Similar to alpha crystallin cages.  Could demo Segger segmentation and proposed tomogram filtering.

 HIV Capsid
 * [http://www.cgl.ucsf.edu/chimera/data/hiv-core-june2011/hivcore.html HIV Capsid] - Illustrates composite model building of HIV conical core particle.  Capsid protein interfaces highly conserved drug target (June 2011 PNAS [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136285/?tool=pubmed paper])
 * [http://plato.cgl.ucsf.edu/chimera/data/tutorials/eman2011 Rous sarcoma virus] - Retrovirus with very similar capsid to HIV.  Did EM fitting and comparison to HIV at EMAN 2011 workshop. 50 minute [http://plato.cgl.ucsf.edu/chimera/videodoc/RousSarcomaVirus/ video].
 * [http://www.cgl.ucsf.edu/chimera/animations/hivrna/hivrna.mov HIV RNA] - Secondary structure of full HIV RNA, I made 3-d model and animation with Chimera script. Nature 2009 [http://www.ncbi.nlm.nih.gov/pubmed/19661910 paper]).  Might add nucleocapsid protein tightly packed on RNA, and collapse RNA into capsid.
 * [http://www.cgl.ucsf.edu/home/goddard/temp/dengue2.mov Dengue virus] - Maturation of dengue virus involves major rearchitecting of capsid.  Chimera animation shows hypothetical model from Michael Rossmann lab.

 Others
 * [http://www.cgl.ucsf.edu/Research/auer/gut-sep2010/ Termite gut] - Segmentation tool demo.
 * [http://en.wikipedia.org/wiki/Myofibrils Muscle filaments], myosin / actin / tropomyosin.  Another good "composite" model example.  Haven't done much with this system yet though.  Recent Roger Craig / Raul Padron [http://www.ncbi.nlm.nih.gov/pubmed/21705660 paper], PNAS July 2011

=== TR&D 3 ===

=== TR&D 4 ===
 * Incremental loading of networks
 * Fuzzy clusters
 * Invoking Cytoscape from Chimera
 * SFLDLoader2??