== Attendees ==
 * Sam, TomF, TomG, Greg, Eric, Scooter, Elaine

= Agenda =
 * Work in progress reports for [wiki:2015-2-5 March 2] demo
 * Discussion of advisory committee meeting schedule

= Discussion =
 * Chimera2 Progress Reports
  * Eric
   * Completed status line API
   * Consolidated initialization call for the struct access module
   * Worked on making radii faster
    * No residue templates were installed, so it was very slow
    * Have issues installing non-python libraries, etc.  Had to fix this to find templates.
    * Opening 1JJ2 (ribosome):
     * .75 seconds open
     * .4 seconds to fetch the radii
   * Did blob operations for filter, intersect (and will need to do merge and some others).
  * Greg
   * Side view now visible
    * View modified to have 2D overlay support
    * Molecule scaling doesn't work right, yet
    * 
  * TomG
   * Updated Oculus rift SDK.  Turned out to be a nightmare (1/2 the calls had changed).
   * Lots of work to get back to getting things to work.
   * Haven't gotten to working with WX, yet.
   * Adding a capable 2D plotting API would be very useful.
 * Advisory committee meeting 8:30 - 2:00.
   * 08:30 Continental Breakfast
   * 08:45 Overview of RBVI Activities and Driving Biological Projects
   * 09:15 Progress on Technology Research and Development Projects
    * Chimera 1 progress (Chimera 1.6 through 1.10, include cellPACK?), 30 minutes
     * Web services
      * Uniprot
      * Loop refinements
      * APBS
      * Multiple sequence alignments
     * Rapid access
     * RRDistMaps
     * RMF
     * Autopack
     * Conrad's Crosslinking interface (?)
    * Chimera 2 and Large models / EM and WebGL, Oculus, 60 minutes
   * 10:45 Break
   * 11:00 TR&D Progress Continued
    * SFLD, 45 minutes
    * Biological context / Cytoscape, 45 minutes
   * 12:30 Working Lunch & Group Photo
    * Oculus and other demos
   * 13:15 Other Center Activities
    * Collaborations, service, training, dissemination. 60 minutes.
   * 13:45 Committee Business
   * 14:00 Adjournment

= Notable Chimera1 Features Since Last !AdCo Mtg =
(distilled from 1.6-1.10 relnotes by Elaine, see [http://www.rbvi.ucsf.edu/home/meng/docs/relnotes/Chimera1-progress.html single-page combined release notes], possible demo/mention in upcoming meeting)

 * as of 1.6:
  * Rapid Access interface
  * fetch Uniprot protein sequence and annotations
  * new ribbon spline options
  * improved transparency rendering (single-layer on by default)
  * better default model colors (pastel rather than saturated)
  * several options for fitting atomic structures into density maps: global search, iterative sequential fitting, symmetric fitting etc.
  * Eric: Plot distances/angles/dihedrals for MD trajectories
  * Eric: Backgrounds from images or using a color gradient
 * as of 1.7
  * interactive shadows
  * glossy lighting default
  * faster loading and graphics
  * Animation timeline
  * interface to Modeller for building missing segments (RBVI web service or local)
  * interfaces to PDB2PQR, APBS, !AutoDock Vina (NBCR web service or local)
  * Eric: Significantly improved !PipesAndPlanks tool
 * as of 1.8
  * show !AutoPack results
  * show Rich Molecular Format
  * REST interface (RESTServer tool)
  * electric field line display for ESP maps (command "measure fieldLines")
  * interactive repositioning of 2D arrows
 * as of 1.9
  * interface to multiple sequence alignment with Clustal Omega or MUSCLE (RBVI web services)
  * "struts" command to reinforce structures for 3D printing
  * "vseries" volume series playback and processing options
  * more efficient save/restore of coordinates in sessions
  * export as Collada
 * as of 1.10
  * protein contact maps color-coded by distance (RR Distance Maps tool)
  * fetch PDB biounit, CATH domain
  * MDA multidomain assembler 
  * Modeller interface allows specifying additional distance restraints
  * plot all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs)
  * show Collada

= Next Meeting =
 *