NIAID Guidehouse/MSC contract May 1, 2023 - Feb 29, 2024

1. General ChimeraX improvements to support NIAID.
   1. Provide support for an NIAID internal app store
   2. Specific improvements to assist NIAID personnel to transition away from the unsupported legacy Chimera program, e.g.:
      1. More GUIs (notably, copy/combine, 2D labels)
   3. Investigate and improve ChimeraX usability for very wide displays and touch screens
      1. Specific focus on the BioViz lab wall display
   4. Work with Enduvo to improve exporting ChimeraX scenes in various formats to their environment.
2. Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development.
   1. Put presets on github
      1. Improve presets documentation
   2. Share code interacting with ChimeraX and NIH3D on github
   3. Continuing support for NIH3D as needed
3. Extend virtual reality support
   1. Investigate molecular viewer for standalone headsets such as Quest 2.
   2. Investigate use of pass-through video with the Quest Pro for multi-person sessions.
   3. Implement a VR ergonomic toolbar and Model panel user interface.
   4. Migrate ChimeraX from SteamVR to OpenXR, the current API standard for cross-platform virtual reality.
4. Explore pedagogical benefits of ChimeraX in VR vs. flat screen
   1. Develop a single web page describing ChimeraX VR capabilities and link to existing tutorials, how-tos, equipment advice.
   2. Describe use cases where VR is advantageous.
   3. Collaborate with the University of Indiana (Katy Borner), UCSF, and NIAID to conduct a task analysis comparing VR vs. flat screen for understanding biological macromolecules
5. Medical Images
   1. Improve DICOM reader by including more data types such as segmentations, and making it more robust by testing against the NCI TCIA repository.
   2. Add ability to “fetch” studies from TCIA
   3. Add support for NifTI format
   4. Add support for NRRD files
   5. Improve VR experience for medical images
      1. Easier manipulation of windowing and leveling, especially for complex curves
   6. General usability improvements for using ChimeraX with medical images driven by TCIA data
6. Outreach
   1. Instructional material and tools documentation.
      1. Detailed instructions for all features shall be provided in a user manual. ii.Written user guides and tutorials shall be available as HTML pages.
      2. Create videos demonstrating new capabilities.
      3. Present webinar and workshop tutorials to train users on existing and new capabilities.
   2. Create video tutorials for how to use multi-person VR.

Attendance at meetings or workshops as required by NIAID

7. Administration
   1. Submit monthly written reports of accomplishments

5/25/2023

Phil, Darrell, Kristen Browne, Andi Bueckle; Scooter, Zach, Selina, TomG, Eric, Elaine

Scooter describes Alex Pico's recent Wikipathways work

Kristen: only one new thing for NIH3D since last time; pdbe biounit url was broken, didn't fall back to pdb. Original ticket was about obsolete entries, should make a new ticket for failure to fall back.

There was an issue with vertex colors in gltf, ChimeraX default gltf save behavior was changed to not include them for single-color objects. Need to get daily build.

Another issue was higher-resolution surfaces from Chimera than ChimeraX. Phil made a table comparing # vertices etc. for several example structures of different sizes, we're not sure why there are so many more triangles from the NIH3D pipeline than in ChimeraX directly. Maybe the sharp boundaries parameter? None of their colorings are per atom, only per chain, by ESP, or by MLP. So they could turn that option off (sharpBoundaries false).

Phil didn't get a chance to look at the pseudobonds-not-connecting issue.

Andi's writing up something but it's not yet ready for discussion.

TomG: maybe the study should use the standalone VR approach with Quest 2. Andi: is this available as a build? He will take a look at Tom's demo

5/11/2023

Phil, Scooter, Zach, Renata, Greg, Tom, Eric, Elaine, Kristin, Meghan

Mehgan: Dmitry at Seattle doing VR work including with clinical applications

Zach: Nifty & NRRD support. TCIA lists ChimeraX as an analysis tool -- Federick labs still sending bugs (lots of interest)

Eric: pseudo-bond error (pseudo bonds don't always connect to the ribbon). Phil is going to review ticket again and see how important it is

Elaine: introduction

Greg: introduction, work on small molecules

Tom: VR standalone, Quest Pro broken, Quest Pro very effective. Discussion about the resolution of the camera in the Quest Pro

Phil: Confusion about Mac install (does Universal installer install M1?)

Kristin: High priority NIH3D issues

• No color modules should always use materials, not vertex coloring (small molecules use vertex colors). Possibly the GLTF writer could potentially switch from vertex coloring to material coloring if the color is all the same
• Resolution of surface models is inconsistent between chimera and chimerax. Chimera is higher resolution.
• Issue with shading and 3D printing (possibly drop normal vectors)