NIAID progress report for group meeting August 25 (last report) - October 5, 2022.

Tom Goddard
October 5, 2022

NIH 3D Pipeline

Zach can describe progress.
Tried opening anonymized clinical DICOM data from Vanitha Sankaranarayanan. Uses lossless jpeg image format that needs gdcm package for reading.
Talked with Jesse Courtier, Chief of Pediatric Radiology at UCSF Mission Bay, who makes augmented reality medical imaging models for cellphone and Merge Cube. Video. Interested in ChimeraX VR.

Sergey Ovchinnikov from Harvard is talking at noon today in Genentech Hall auditorium. He developed ColabFold.
Ellen Zhong, developer of cryoDRGN, will be talking about machine learning methods at the November 1-4 CZI Imaging Institue cryoET meeting in Mountain View.
Utz Ermel, developer of the ArtiaX cryoET particle visualization ChimeraX plugin will be talking at the CZI cryoET meeting.
I will talk about cryoET visualization needs at the CZI cryoET meeting, hosted by Dave Agard, Bridget Carragher and Clint Potter.
Tristan Croll visited Altos Labs in Redwood City on September 13, had lunch with him and discussed OpenMM plans.


Wiggle cryoDRGN viewer by Charles Bayly-Jones	My initial cryoDRGN viewer

Elaine presented group meeting journal club on cryoDRGN software.
Made cryoDRGN viewer of uMAP conformation space and representative maps.
Requested suggestions for cryoDRGN viewer in their GitHub issues.
Ellen Zhong the cryoDRGN creator responded.
Charles Bayly-Jones (Monash University) who has made a much better ChimeraX cryoDRGN viewer called Wiggle responded.
Charles has 4 tutorials on Wiggle on YouTube.
Wiggle can compute new volumes using cryoDRGN neural net using PyTorch.
Charles proposed we combine efforts.
Working on getting Charles to put Wiggle on Toolshed. Currently he has complex install instructions from GitHub.

Errors running cryoDRGN turned out to be caused by memory errors reading 50 GB files.
AlphaFold also has in the past year failed many times with errors reading 100 GB database files.
SHA checksums on large files showed consistently wrong values.
Sent computer back to HP and they replaced the memory (3 of 4 DIMMS).
Working correctly now.

New machine learning structure prediction method for large symmetric homo-multimers based on AlphaFold.
Read UniFold Symmetry preprint.
Should install and test as possible ChimeraX web service.

Switched ChimeraX AlphaFold database search from BLAT to my kmer-search code
AlphaFold database will release version 4 in coming weeks fixing poor predictions in 4% of entries. Details at end of FAQ. We will update ChimeraX to use v4.
Read AlphaFold / cryoEM paper analyzing correct and incorrect predictions by Matt Baker (formerly in Wah Chiu's group).

I attended RCSB computed structure models (mostly AlphaFold) workshop, 4 talks/tutorials.
1 million AlphaFold models now available through standard RCSB web search.
RCSB web site now offers ChimeraX-like capabilities:
- Coupled sequence-structure viewer.
- Structure alignment.
- Binding site motif searches.

Gave VR hemoglobin sickle-cell anemia demo to three UCSF biophysics students using Quest 2 headset and wifi.
Analyzed jitter in VR with Quest 2 headset. Much less jitter at 90 Hz refresh rate instead of default 72 Hz.
Tristan and head of software at Altos software engineering Bikash Sabata are excited to get VR working well with ISOLDE.
I've tried OpenXR which appears to be the future VR API for running on headsets from different vendors. Currently we are using SteamVR. OpenXR is the Meta's API, they deprecated their proprietary APIs. Valve, developer of SteamVR, is also supporting OpenXR.
Quest Pro heaset will be released this month. High resolution color pass-through camera, higher resolution screens 2160 by 2160, eye tracking, face gesture tracking, pancake lenses for thinner headset, hand-controllers that track with 3 embedded cameras instead of IR light ring. Cost expected to be > $800.
Studied GLTF export of vertex and texture colors for Enduvo VR software for Phil Cruz. Phil introduced me to Enduvo developer Justin Drawz to improve color handling.
Borrowed ISOLDE ligand parameterization for molecular dynamics to test MD of ligands in binding sites in VR. Aspirin phosphlipase example. Will see if Jacobson lab is interested.

Made a Mole file reader (json) for ChimeraX to show channels computed by web server for Phil Cruz.

Made phage tail non-uniform sheath contraction Python code for collaborator Andy Sen.
Made a tutorial on assembling multiple PDB models to animate phage T4 needle injection.
Added ability to export assemblies in mmCIF files using the sym command for Pranav Shah.

Helped Brian Hudson at RCSB with slow ChimeraX map rendering on CentOS 7 with network file system.
Takes a minute for ChimeraX to start loading its thousand Python files.
They will look into alternative computer hardware.

Made Mac universal builds (includes ARM and Intel binaries in one distribution).
Mac universal daily builds on download page since Sept 23 and ARM daily builds since July 22.
Universal, ARM and Intel versions ChimeraX 1.5 will be released.
We will continue to support macOS 10.14 (2018) as oldest Intel Mac version.

I attended the CZI Annual Meeting for Open Science associated with our CZI grant by Zoom.
Interesting discussions of how to make open source software sustainable by encouraging a community making pull requests.
Discussion of how to make software accessible to Africa and Latin America by providing French and Portuguese training material.
Darrell Hurt suggests we make a ChimeraX intro tutorial video in French and try it with the NIAID's African ACE project in Mali.

Woonghee Lee is the developer of NMR program Poky and NMRFAM Sparky which are the successors of our UCSF Sparky software.
He asked for an in-person ChimeraX tutorial at University of Colorado, Denver, all expenses paid by them, in April or May.