Attendees

Conrad, Elaine, Eric, Greg, TomG, TomF

Agenda

• ChimeraX public pre-release
  • Cache behavior
  • Mac distribution method
  • Linux distribution method
  • Download URL
  • Compiling source packages
• Best strategy on how to update pypi dependencies
• Chimera 1 update
  • New EDS URL
  • New (to us) Dunbrack rotamer library

Discussion

• ChimeraX pre-release
  • pdbe/pdbj still need to be documented in open command
  • Cache behavior
    • CCD cache location should be documented and managed manually
    • No mechanism (for now) for checking whether cached file is up to date
  • Mac distribution method
    • TomG will take a look at why dragging from dmg results in app failure on first open
    • TomG will update the dmg compression method
  • Linux distribution method
    • Sticking with .tar.gz
    • Greg will see if any libraries are missing for CentOS 7
  • chimerax-users@… will be separate from chimera-users@…
  • Download URL
    • Will be added to home page
    • Will be "www" not "preview"
• Best strategy on how to update pypi dependencies
  • Greg changed install command so that updates will not be installed if sufficiently new package is already installed
  • Test new package versions periodically. What is the easiest way of doing this? Get list of updated packages weekly.
  • Change all >= to == now
• Chimera 1 update

Action Items

• TomG will look into Mac distribution method
• Conrad will create ChimeraX users mailing list
• Elaine will create feedback page to reference mailing list once it is made
• Eric will add Help->Contact Us menu item
• Conrad will make symlink from /download.html to /docs/download/chimerax.html
• Eric will change dependencies from >= to ==
• Greg will write a script to identify pypi updated packages weekly

Alpha-release features remaining to be completed (from site visit presentation)

• Clean up cache directories (too many of 'em as it stands)
• Sequences and alignments
• Saving and restoring sessions
• Hydrogen bond finder
• Full Toolshed semantics

Additional alpha-release possible features

• Write PDB format
• Improved writing of mmCIF format

High priority tickets for alpha-release

• #473 Create Linux installer and distribute necessary system libraries. Greg
• #469 HTML link to open local file should be interpreted relative to HTML file location. Greg

Medium priority tickets for alpha-release

• #472 ChimeraX "open" command format-specification issues. Greg
• #418 problems with help command new-viewer option. Greg
• #412 Fails to start on Mac with comma in app name. Conrad
• #370 links from Help viewer to external pages give traceback in Qt version. Greg
• #235 Compressed session files should have suffix .cxs instead of .cxs.gz. Greg
• #69 Atom spec parsing does not preserve model or chain order. Conrad

Low priority tickets for alpha-release

• #449 Volume planes on multiple data display is erratic. TomG
• #447 Transparency command on volumes undone when contour level changes. TomG
• #417 Help viewer suggestions. Greg
• #367 Error after deleting all atoms. Eric
• #299 Ability to add tool-specific keywords to open command. Greg
• #236 Saving a session with an unknown model type gives an error. Greg
• #439 Fix signing of Windows installers. Conrad
• #502 Findclash misleading and wrong. Conrad

More discussion needed

• #342 Convert from cxhelp/cxcmd schemes to http scheme. Conrad
• #259 Tools should not save in sessions by default. Greg
• #251 Session save/restore slow. Greg
• #61 Rendering takes minutes, Mac Nvidia Geforce GT 330M graphics. TomG

Check and close

• #411 Copyright messes up Mac installer html. Conrad
• #378 Atom spec parsing stops at non-whitespace. Conrad
• #327 Log stops updating beyond 2 Mbyte size. TomG
• #318 Colourlovers palette message logged above command. TomG
• #284 handle mmCIF with missing sequence information. Greg
• #283 Curved helix tubes. Conrad
• #239 File... Save GUI save image adds ".cxs" before image suffix. Greg
• #214 Save image dialog bitrot. Conrad
• #198 finish session molecular data save/restore. Conrad
• #150 Ribbon slow creation. Conrad
• #140 Provide common database fetching routines. Greg
• #70 log tool doesn't cleanup when deleted. Eric
• #62 Register file fetch using database name. Greg
• #49 Better warning message if oculus fails to start. TomG