Progress report May 11, 2023 - July 5, 2023

Tom Goddard
July 6, 2023
Group meeting

Possible collaborative projects

Dyche Mullins and Laura Cheradame - segmenting filaments in tomograms

• Met with Dyche and Laura and looked at tomograms DNA damage in mouse neurons.
• They are interested in trying machine learning segmentation to distinguish cells with damaged DNA from normal cells.
• By eye we can see filaments in the damaged DNA puncta.

Muyuan Chen in Wah Chiu's lab, virus animations

• Muyuan used ChimeraX exported models with Unreal Engine level-of-detail capabilities to animate virus scenes with tens of millions of atoms. Video.

Helen Berman and Jitin Singla - tetrahedron protein depictions

• Meeting Helen by Zoom about once every few months for her Inner Space project at USC, animating pancreatic beta cells for VR.
• Jitin Singla's student writing ChimeraX bundle to depict each residue as a tetrahedron.
• Next Zoom meeting July 18.

Dmitry Lyumkis, Salk Institue cryoEM, fscplot extension

• I helped update Chimera fscplot tool to ChimeraX.

Max Krummel, embed 3D light microscopy in web pages

• Made web page explaining how to embed ChimeraX GLTF scene using Google Model Viewer.
• Max also interested in showing 3D tumor cells with Quest VR.

John Sedat, stereo visualization of low dose CT scans

• John has noise filtering methods to allow medical CT scans at 10x lower dose.
• Trying to promote stereo visualization in clinical setting.
• Met with John and had a few phone calls to discuss use of VR for stereo viewing.

Tristan Croll, ISOLDE on Apple Vision Pro AR headset

• Discussed visionOS for running ISOLDE.
• Tristan says Altos Labs software head interested and could hire a couple Apple developers.
• Discussed continuous Chimerax scene updates to standalone VR to avoid speed bottlenecks.

Selina Liu, locating ions in cryoEM maps

• Selina developed ML in Keiser lab to identify ions in cryoEM maps near atomic model.
• This might make an interesting ChimeraX tool.
• Similar to Phenix douse that finds waters in cryoEM maps near atomic model.
• Use UMAP visualization of training and testing results.

NIAID NIH 3D web site and GLTF and surface resolution

• Tried NIH 3d web site, downloaded cellpack virus and viewed in ChimeraX.
• Made various ChimeraX GLTF export improvements for Kristen Browne.
  1. Remove vertex colors for single color objects.
  2. Added flat_lighting option.
  3. Added backface_culling option.
• Investigated jagged NIH 3D molecular surfaces in meetings and emails.
• Sped up million atom molecular surface calculation 100-fold.
• Considering mesh decimation, sharp-edges, offering multiple NIH 3D resolutions.
• Investigated GLTF vs ChimeraX color differences, linear RGB vs sRGB, Kristen Browne

GLTF viewer colors	ChimeraX colors

AlphaFold updates

• Colab now offers A100 GPUs at market rate ~$1-2/hour that ChimeraX AlphaFold prediction can use.
  • Tested running 2000 residue alphafold prediction with A100 gpu on google colab.
  • Tweeted and made YouTube video showing how to use A100.
• Added maxPae option to alphafold contacts command, Ah-Ram Kim

Alphafold prediction web service maintenance

• Google Colab updates break AlphaFold prediction several times per year.
• Colab update from Python 3.9 to 3.10 broke energy minimization because old OpenMM required by AlphaFold was not available on 3.10. Required ColabFold fixes to use newer OpenMM.
• Reported new ColabFold bugs to Sergei Ovchinnikov reports, logging.
• Sergei accepted my earlier ColabFold pull request allowing me to simplify Chimerax prediction script.
• Fixed alphafold prediction openmm install error cause by bioconda update.
• Helped a few users recover failed alphafold downloads.

Meetings

Stanford cryoEM Workshop

• Gave 2 hour intro cryoEM tutorial to 50 in-person and 50 online participants, atp synthase, at SLAC cryoEM workshop hosted by Wah Chiu.
  • 30 minutes of questions and requests at SLAC workshop.
  • Ported mcopy command from chimera to chimerax
  • Ported volume filter gui, Mike Schmid request
  • Added volume sharpen command.

Fraser lab / Phenix / ChimeraX 1 day ensemble modeling meeting

• Progress in software for ensemble modeling.
• In maps with better than 1.8A resolution can see alternative atom locations for 40% of residues.

    How do we improve the modeling of ensemble-based models?
  
    Location: UCSF Mission Bay Genentech Hall S202
  
    9:00 am: Introduction (Jaime Fraser & Paul Adams)
    9:15 am: Multiconformer modeling of X-ray and cryoEM structures with qFit (Ashraya)
    10:15 am: Break
    10:40 am: Measuring map-model fit and resolvability with Q-scores (Greg Pintilie)
    11:10 am: Phenix Team: Quantum Refinement (Nigel)
    11:45 pm: Discussion on new CIF model with alt confs (Jaime)
    12:10 pm: Lunch at SF Kebab
    1:10 pm: ChimeraX: Ensemble capabilities (Eric Pettersen)
    1:40 pm: Multi-part bulk solvent and Model-to-Map Fit Validation (cryo-EM) (Pavel)
    2:10 pm: Modeling partially occupancy water molecules (Stephanie)
    2:40pm: Bayesian optimization of multiple models in cryoEM maps (Matt Hancock, Sali lab)
    3:10 pm: Closing remarks
  
  

• Tried Quest VR visualization of large number of alt-locs (33%) in transaldolase PDB 6zx4.
• Standalone VR may be useful for discussions of alt-loc functions.

Quest 2 multi-person AR meetings

• Added multiperson AR or VR meetings to Quest molecular viewer app LookSee.
• 2 or more participants see the same molecules, maps and can move and scale.
• Any participant can open new models which are copied in seconds to others.
• Mike Schmid at Stanford will try it with tomograms.
• Andreas Bueckle, NIAID VR user study designer will try it.
• Learned about async/await programming (C#, also in Python) to handle network meeting messages.

Miscellaneous ChimeraX improvements

• New ChimeraX recipe how to realign map symmetry axis to z, for Tianyang Liu.
• Added move-to-center mouse mode, for Yang Lee.
• Color large structures when opened by polymer instead of single color.
  
• Made C-alpha RMSD coloring how-to video and tweeted, for Matthias Vorlander.
  

ChimeraX daily now using Python 3.11

• Zach updated ChimeraX from Python 3.9 to 3.11.
• Had to fix a handful of problems (e.g. no implicit casting float to int).

New computers

• New VR machine with Nvidia 3070, setup in corner in vizvault -- multi-person VR is working. Windows 11.
• New ML machine in treasure room, Nvidia 4090 (24 GB memory), Ubuntu 22. AlphaFold. Selina is training lung tumor ML on it.