NIAID progress report for group meeting April 7 (last report) - May 18, 2022.

Tom Goddard
May 19, 2022

New Contract

• New NIAID contract started May 1, 2022. Thanks to Scooter.

NIH 3D Pipeline

• Eric can describe progress.
• Asked RCSB and PDBe about new biounit assembly files and urls fetched by ChimeraX.

DICOM

• Zach can describe progress.
• Zach and I tried viewing Jason Rubenstein heart echocardiogram DICOM times series in VR.
• Still need to help Jason with VR.

AlphaFold predicted aligned error (PAE) plots

• Allowed reading ColabFold web site PAE plot json files, they use a different format, Thibault Tubiana
• Show residue numbers in status line when mouse over plots, Phil Cruz
• Allow drag on PAE plot to select structure residues instead of color them, Jan Gebauer
• Allow coloring PAE plots to match structure colors, Gerard Kleywegt
• Changed PAE plot colors to rainbow to better show gradations, Jan Gebauer
• Added divider lines in plots between chains, Jan Gebauer
• Added minimum number of residues option for computing PAE domains.
• Assigned domain numbers to residues for PAE domains for use in commands (e.g. coloring, selecting domains), Tristan

AlphaFold

• Gave AlphaFold cryoEM training at Stanford for Wah Chiu class, insulin receptors (April 25)
• Found AlphaFold could predict binding of 9 amino acid signal sequence in encapsulin-ferritin complex.

VR

• Zach and I did Byer's Lecture VR demo in Genentech Hall atrium for Natalia Jura, HER2/HER3 cancer complex.
• Zach took Oculus Rift S home to get familiar with ChimeraX VR.
• Looked into vive focus 3, new standalone VR headset, Phil Cruz ordered one
• Fixed clipping problem with mixed reality capture with RealSense depth camera.