Attendees

TomF, TomG, Greg, Eric, Scooter, Elaine

Agenda

• Work in progress reports for March 2 demo
• Discussion of advisory committee meeting schedule

Discussion

• Chimera2 Progress Reports
  • Eric
    • Implemented HTML reply log, including images
      • After commands are executed, a thumbnail is shown of what the scene looks like
    • Implemented status (status messages now show up)
    • Just completed merging of blobs
    • Wants to work on "fancier" parts of status logging
      • Go away after a period of time
      • Keywords (followWith, etc)
      • Alignment of status line with command
    • HTML window doesn't work very well on Linux
  • Greg
    • Logging widget does not work on Linux
      • WX html demo works but doesn't work on in the context of Chimera2
    • Working on side view
      • Will eventually support changing camera modes
      • Some issues with stereo support
      • Currently not working correctly -- side view graphics show up in main window
      • Side view is also orthographic rendering, which is not currently supported by Chimera2
      • Will work with TomG on this
  • TomG
    • Oculus Rift on Chimera2: haven't tried, yet. Will need to do a lot of WX stuff to make it work. Was able to find WX function calls to do the necessary things.
    • Did work on supporting cell motion through oculus rift. Currently you have to jump through a number of hoops. Tom is working on making this simpler. Currently, it's pretty fragile, but Tom has been working on making it less fragile.
    • Add space navigator port to March 2 list
• 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 ​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

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