Attendees

• Conrad, Elaine, Eric, Scooter, TomG, Greg, TomF

Agenda

• Discussion points from January 9th meeting:
  • Discuss Elaine's email about open command
  • Should we avoid sub-sub-commands altogether? (this affects some of the "may's" and "might's" listed here: ​https://plato.cgl.ucsf.edu/trac/ChimeraX/wiki/2017-01-09)
  • Need to discuss the style command
  • Think about overlap between view, position, and camera commands
  • Should we do anything further about "~" or just keep them as aliases?
  • Need to clean up usage hints
  • "objects" vs. "atom-spec". Usage separates the two concepts (e.g. see select), but help documentation merges them.
  • Should "entity atoms", which means the same molecular entity, be part of the atom-spec?
  • Need more discussion/revision for select only option
  • Need to think about visualization of nucleotides

Discussion

• Changes to open command:
  • all booleans in open (AND all other ChimeraX commands) should take true/false argument
  • keyword changes:
    • trajectory to coordset
    • series to vseries
    • smartInitialDisplay to autoStyle
    • oneAlignment to alignment
• To avoid sub-sub-commands:
  • vop to be replaced by volume
  • sop to be replaced by surface
  • device command to be added and will include subcommands
  • remotecontrol will have subcommands, including rest
  • measure command to be added with subcommands (distance, buriedarea, sasa, etc.)
  • debug command to be added with subcommands (dumpspec, sdump, test)
• Style command:
  • size command to be merged into style command