Attendees

• Sam, 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
    • 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 ​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