Attendees

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

Agenda

• Action items
• Chimera
  • 1.13.1 release
    • catastrophic failure on protein residue with all zero coordinates
• ChimeraX
  • Wildcard/regex/case matching in atomspec (Eric)
  • Installers for CentOS/Redhat
  • RBVI bundles on toolshed
  • Documentation strategy
  • Change build process to trim down list of bundles in standard release while still testing toolshed-only bundles

Discussion

• Chimera 1.13.1.
  • So far so good. Let it simmer a while more.
  • Tristan's example from CASP entry with all zero coordinates in a residue causes Chimera to "exit abnormally"
    • Ignore for now
• ChimeraX
  • Changing log behavior
    • Reorganize "save" command:
      • Remove "metadata" and "verbose" from main command
      • Move "savePath" and "forDemo" into a "log save" subcommand. ("forDemo" or "executableLinks" does not change user preference.)
      • Move "warning" and "error" options into "log setting" (non-sticky) subcommand and add in Settings.
    • Try out new syntax and discuss again next week
  • Wildcard matching
    • Use file globbing syntax for atomspec wildcards, replacing the '=' in Chimera 1 with '*' since '*' should no longer appear in atom names
    • For attribute testing, use four operators: '=' and '~'. '=' is a string match. '==' is a case-sensitive string match. '~' is a glob match. '~~' is a case-sensitive glob match
  • Installers for CentOS/Redhat
    • Up on web site. Tristan may be testing it soon.
  • Putting RBVI bundles on toolshed
    • Conrad showed toolshed rbvi bundle release page
    • Scooter says Cytoscape app store revamped recently, ChimeraX should use new Django code.
    • Fix "New version" section of candidate bundles
    • Add "make sync" to daily build
    • Push to production site
  • Documentation strategy
    • Current layout below
    • What layout do we want?
    • Use virtual overlay, with make target for resynchronizing symlinks

docs	user	commands	close.html
		tools	filehistory.html
		formats	bild.html
src	bundles	bundle_name	docs	user	commands	my_command.html
					tool	my_tool.html
					formats	my_format.html

Action Items

• Greg will implement documentation virtual overlay symlink target
• Implement wildcard matching. Eric will create a ticket for Conrad.
• Send announcement on Chimera mailing lists regarding Mojave fix in daily and candidate builds (Elaine and Eric)
• Conrad will create ticket listing stable APIs