ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg, Mikhail

October 9, 2023

Agenda

• Pat Rynkiewicz wants to distribute ChimeraX with docker and his MD.
• Log slow to update when it gets long, Tristan ticket #9909
• Worm ribbon implementation, ticket #9942
• Tristan Toolshed install dependency issues, Ticket #9861, blocking Clipper update #9786
• Tristan, bundle version number not reported correctly. Ticket #9873
• ChimeraX 1.7 release schedule
• Task Manager progress
• Install Grafana on plato to monitor web services.
• ViewDockX port to Qt progress
• How does ChimeraX code that needs an optional bundle on Toolshed query for it?
  • Implications for library distribution
• Wording of LGPL notice / which files to change
• Toolshed website spinning progress never goes away.
• Release initial ChimeraX library on PyPi or Conda
• How long should code commits be added to release branch after release?
• Back up the Chimera build machine to a solid state drive, Windows 7.
• ChimeraX Ideas milestone clean-up.

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Discussion

• Docker distribution of ChimeraX
  • Pat Rynkiewicz asked on the Chimera mailing list whether he can distribute ChimeraX in a Docker image with his MD tools which somehow use ChimeraX.
  • TomG asked him how he uses ChimeraX (gui / nogui), and said we don't allow redistribution except by special arrangement.
  • Not sure ChimeraX can be run in gui mode from Docker.
  • We will wait to get more info from Pat.

• ViewDockX
  • Eric asked that Mikhail not attach viewdockx javascript to email since that makes ProofPoint delete it. Mikhail will use google drive links in future.
  • Mikhail demonstrated viewdockx reading mol2 and displaying table in qt.
  • Greg suggested using more tightly spaced columns.
  • Mikhail is working on Plot and Graph buttons and on show/hide column checkbuttons.
  • Eric suggests restoring old sessions would be useful.

• Log slow to update for Tristan
  • Tristan observed ISOLDE commands hand .25 second pauses due to long log panel being refreshed.
  • We need a reproducible example to see how serious the problem is. Eric will ask Tristan for a session file.

• Worm ribbon depiction
  • Eric will survey Chimera worm ribbon code to see how it was done: what was residue radius attribute called? Is it only at whole structure level? Is radius cubic splined? Is there any chimera command to control it?
  • Need to decide if ChimeraX will do it the same as Chimera or if there are any different capabilities desired. Eric will ask Elaine to weigh in.
  • Eric can implement C++ atomic data structure attributes and render by attribute command to set the radii.
  • Then Tom can implement the rendering, which he thinks is not too much work, 1 day.

• Toolshed bugs effecting Tristan
  • Tristan has been hampered updating Toolshed bundles by various bugs.
  • Tom asked Tristan to update Clipper for use in daily build for NIAID (Phil Cruz) but he was not able to due to Toolshed problems
  • Greg says fixing these toolshed problems is currently his top priority, hopes to resolve them by the end of this week.

• ChimeraX 1.7 release schedule
  • We will make release candidate October 30 unless discussion at that ChimeraX meeting determines it is not feasible.
  • Typical release candidate to actual release time has been about 6 weeks, but can be as short as 2 weeks.
  • Most likely release time is in first half of December.
  • Tom is working on OpenXR, Eric on Fetch by Id, Greg on Toolshed bugs and Flatpak, Zach on dicom rendering planes using volume copies, Mikhail on ViewDockX port from html to qt.
  • Tom estimated 2 weeks to make openxr available in 1.7. ViewDockX port will likely take longer but could be done in a month.
  • We will drop features if needed to maintain release schedule since there are many bugs that have long been fixed that continue to be reported.

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Action Items