Attendees =

TomF, TomG (remote), Eric, Greg, Sam, Elaine

Agenda

• Status update

Status update

• Three tasks
  1. Add graphical attributes to molecular data structure. (Eric)
     • Significant progress but also technical problems requiring more time than anticipated. Expect original set of attributes to be done tomorrow. After that, will work on setting atomic radii. Discussion with TomG of putting all numpy stuff into one file, which would require significant rearrangements.
  2. Modify MMCIF/PDB readers to output new molecular data structure. (Greg)
     • Much code in place. Currently getting residue templates via URL since web services aren't yet ported to Chimera2.
  3. Render the molecule. (Tom)
     • Have added rudimentary rendering that doesn't use graphical attributes, just shows all atoms as spacefilling in element colors. This is useful for checking data loading and has revealed an issue with setting center of rotation. Can start using the graphical attributes once they are available.
     • Will also add cylinders to allow bond visualization. Discussion with Greg that things should be put into Geometry so that they will work without GUI.
• Conrad will finish up the Tools manager and then work on atomspec parser
• Defer for later discussion: whether to have wire displays in Chimera2

Chimera1 things

• TomF said that Nicholas Polys at Virginia Tech complimented our X3D export and says he uses it all the time
• It may be worth revisiting our Collada export to see if there has been any progress in standardization or how various viewers handle the files from Chimera

Next Meeting

• Further status updates at Monday meeting