NIAID contract progress February 2, 2023 - March 30, 2023

Tom Goddard
March 30, 2023
Group meeting

NIAID contract progress

• Eric - NIH 3D pipeline
• Greg - Improved mmCIF reading
• Zach - DICOM
• Elaine - Documentation
• Tom - Virtual reality and machine learning for cryoEM

NIAID 2023-24 contract

• NIAID contract expired end of February.
• Contract not yet renewed as of mid-March according to Phil and Meghan.
• Proposed statement of work Google doc.

Virtual reality

• Helped Phil Cruz with two person VR demo (without internet) at Nitric Oxide Gordon conference (molecular mechanisms of blood pressure regulation), using "next" command for power-point style VR demos.
• Fixed VR click range, was mistakenly 5 meters instead of 5 Angstroms, now 10 cm.
• John Sedat investigating Varjo retina resolution VR headsets for chromosome tomography. Only military has these $10K headsets for simulated airplane cockpit training, so hard to get access.
• Made many gltf improvements: transparency, textures (volume data, medical imaging, text labels), mesh lines, metallic and roughness lighting.
• Discussed VR user study ideas at bi-weekly NIAID meeting with Andi Bueckle at University of Indiana, and Phil and Meghan

Standalone VR Quest 2 and Pro headsets 2 for molecules and image data

Quest Pro with pass-through video.	LookSee Unity app user interface.	ChimeraX Send to Quest tool.

• Wrote vr viewer Unity app LookSee for quest 2 and quest pro standalone for gltf scenes.
• Studied quest maximum scene triangles, texture fill, number of lights
• Tried color pass-through video with quest pro showing molecules
• Investigated transfering gltf scenes from computer to quest: google drive, ftp, adb
• Gave VR demo at West Coast Structural Biology workshop at Asilomar, Mike Schmid, paxlovid drug resistance
• Made initial LookSee web page.

Other ChimeraX progress

Collaborations

• Tristan Croll, Altos Labs: Testing new QScore tool (on Toolshed) to quantify per-residue fit quality in map.
  

  Plot shows per-residue quality of fit in map. Clicking plot shows corresponding residue.

• Shawn Douglas, Konlin Shen, Hamish Todd: Tried RealTalk / Dynamicland installation in S474.
  

  Futuristic workbench computing for developing DNA origami wet lab research protocols. Interfaces through projectors and cameras.

• Brinda Vallat, Rutgers: Wants PDB IHM visualization in Mol*, planning a developer meeting.
• Klim Verba, UCSF: Make VR usable with ISOLDE.
• Helen Berman, USC: World in a Cell pancreatic beta cell VR, tetrahedron protein depictions.
• Klim Verba, Helen Berman: Depicting molecular breathing, use OpenMM with B-factor scaled random forces.
• Paul Korir and Martin Schorb, EMBL: Made EMDB segmentation file format handle bounding surface segmentations (different from per-voxel segmentations).

ChimeraX Tutorial Presentations

Transparent surface by default casts no shadows.	With shadows.	Shadows make interior structure black.	Interior structure ignoring shadows.

• Soft lighting with transparency for Scott Stagg.
• Made a color by C-alpha RMSD how-to video on YouTube and tweeted.
• Gave Quest Pro VR/AR paxlovid drug resistance demo, 7 biophysics student applicants.

Color byC-alpha RMSD tutorial.	Paxlovid (pink) drug resistance (orange) and compensatory (green) mutations on SARS-CoV-2 main protease (brown).

Machine learning maintenance

• Fixed error in alphafold blast when loading a matching structure, Ulrich Baumann
• ChimeraX AlphaFold survived Google Colab updating (unannounced) from Python 3.8 to 3.9. In November the unannounced updated python 3.7 to 3.8.

Medical Imaging working group meeting, March 6

• Meghan McCarthy suggested Zach and I attend this medical imaging visualization meeting.
• Medical working group participants:
  • Led by Nicholas Polys, Director of Visual Computing for Virginia Tech Advanced Research Computing
  • Michael Aratow - Chief Medical Information Officer of San Mateo Medical Center, working group co-chair
  • William Glascoe - developing 3D Body Processing standards in IEEE
  • Anita Havele - Executive Director, Web3D Consortium
• MONAI segmentation platform discussed.
• NIH Advanced Research Projects Agency for HealthARPA-H funding for high risk projects.
• Discussed Health Level 7 (HL7) clinical data transfer standard, and 3DMD volume capture standard.
• ImageTextureAtlas X3DOM class for tiled volume rendering.
• Virtual Natural History Museum web site of animal medical scans using X3DOM web volume viewer.

Miscellaneous

• Added volume export from Chimera to Chimerax.
• Added tugging and energy minimizing ligands using openmm and ligand parameters for 21000 PDB ligands from Phenix team, Nigel Moriarty.

Interactive molecular simulation of ibuprofen in fatty acid binding protein