Attendees

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

Agenda

• Continuing discussion from January 23rd 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
  • Ribbon (cartoon) lingering issues/suggestions ​Elaine's summary
  • What is the policy regarding "~"? How do we negate a command? Should we do anything further about "~" or just keep them as aliases?
  • Session saving in alpha release: continue to use pickle or move to msgPack?
  • 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

• view/position/camera -- "camera" OK as is, TomG to merge "position" command into "view" command
• Lingering ribbon issues ​Elaine's summary -- to be continued in a week or two
• "~" policy: Tilde should be provided for backwards compatibility only. Otherwise there must be a English word for negation of a command, e.g., show and hide. Other examples of correct behavor:
  • cartoon hide
  • hide cartoon
  • ~cartoon (alias)
  • surface hide
  • hide surface
  • ~surface (alias)
• This means adding new representations like nucleotide means updating show and hide.
• Keep pickle at least for now and have future ChimeraX versions able to read previous version of save format. E.g., release 1.0 will be able to read beta release sessions but may not be able to read alpha sessions.

Action Items

• Add magic numbers to session files - Greg & Conrad
• TomG to merge "position" command into "view" command
• Conrad will continue working on ribbons
• Conrad will add "cartoon hide"
• Greg will add "hidden" keyword to command registration