Attendees

Elaine, Eric, Greg, TomG, TomF, Conrad

Agenda

• Commands (what's next, syntax, etc)
• Revisit colordef vs color define
• Review Andreas' list
• Should we change Python package from "chimera" to "chimerax"?
• Updates [All]

Discussion

• Documentation needs to be split into two types:
  • User documentation by Elaine, who tests the commands in addition to documenting them. These are also intended for consumption by users and therefore should not include experimental, incomplete commands (e.g., saving sessions without molecular data support).
  • Programmer documentation by Eric, TomG, Greg and Conrad. New commands should have their intended functionality and syntax included in their doc strings so that Sphinx picks it up. We can then discuss what the written proposal instead of having only verbal descriptions (sometimes several different versions).
• "usage" output for commands with enumerated values
  • "usage style" currently yields "style atom_spec atom_style", which is not very useful if you do not know the legal values for atom_style. Enumerated values should be listed on the next line, e.g.,

    style atom_spec atom_style
    atom_style: one of sphere, stick, ball
    

  • Enumerations should be listed even if the registered argument is Or(empty, enumeration)
  • "lighting" should be fixed to use enumerated "preset" options instead of using independent keywords. This would make usage work as expected and make specifying multiple presets an error.
• "format" argument in "save" command uses format name ("session", "jpeg", "png") and not suffix ("cxs", "jpg", "png"). Suffixes are explicitly not included as aliases to minimize cluttering up the command help/usage.
• "position" and "setModelPosition" keywords to "view" command are split out into their own command
  • Two proposals were made:
    • Five commands: view, clip, position, camera, cofr
    • One command with subcommands: view, view clip, view position, view camera, view cofr
  • Five-comand version was selected
  • "view" command will eventually be extended to include options to use only some components from a view, e.g., just the camera and clipping planes, or just model positions but not camera, etc.
  • New command "position" will be:
    • position <no arguments> = list all current position information for camera and models
    • position camera <12 numbers> = set camera position
    • position models <model_spec,12 numbers>[,<model_spec,12 numbers>]* = set model positions
    • position initial <model_spec> = reset model position to initial orientation
  • "view initial model_spec" will be removed
  • "view orient" will be kept (reset camera orientation)
• Meeting adjourned
• Revisit colordef vs color define
• Review Andreas' list
• Updates [All]

Action Items

• Tom's list:
  • Split view command
  • Fix lighting command
• Greg's list:
  • Make "view list" and "view delete" subcommands