ChimeraX Grant Funding Specific Aims

January 23, 2023

R01 September 2022-2026 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling

Resubmission ​plan. Original plan and aims

• Aim 1: Develop visualization and analysis tools for atomic structures and associated data, including assemblies, ensembles, maps and sequences.
  • 1A: Analysis capabilities (.45 FTE)
    • Prepare structures for docking/modeling.
    • Sequence-structure analysis.
    • Dimensionality reduction.
  • 1B: Dissemination of results (.45 FTE)
    • Animations.
    • New glycan depictions.
    • Improved interoperability with wwPDB repositories.
• Aim 2: Develop visualization and analysis tools for electron microscopy of molecular assemblies and cells.
  • 2A: Developments for electron microscopy of molecular assemblies (.35 FTE)
    • Machine learning structure predictions.
    • Visualization of molecular conformational heterogeneity using machine learning.
    • Interactive molecular dynamics for fitting atomic models in maps.
    • Faster map contouring and masking.
    • Additional building and validation tools.
  • 2B: Developments for electron tomography of cells (.53 FTE)
    • Improved volumetric visualization using lighting.
    • Visualizing, quantifying, and creating segmentations.
    • Analysis tools for subtomogram averaging.
    • Virtual reality visualization of tomograms.
• Aim 3: Provide a diverse software foundation enabling labs around the world to develop and distribute new molecular and cellular structure analysis software.
  • 3A: New capabilities for plugin development (.35 FTE)
    • A standard platform for machine-learning algorithms.
    • Simple programming to access web services.
    • Providing complex calculations with good user experience (long-running calculations).
    • Programming examples.
  • 3B: Expanding the distribution of plugins (.17 FTE)
    • Utilizing the PyPi and Anaconda Python package managers.
    • Cloud-based building of ChimeraX and plugins.

NIAID contract, March 2022 - 2023

​Statement of work, meeting ​minutes

• General ChimeraX improvements to support NIAID.
  • Specific improvements to assist NIAID personnel to transition away from the unsupported legacy Chimera program.
• Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development.
• Virtual reality for molecular structure, cryoEM and medical imaging.
• CryoEM modeling utilizing machine learning structure prediction.
• DICOM
• Outreach
• Administration

Phenix R24 May 2021-2026 - Phenix interaction with ChimeraX

Plan

• Implement ChimeraX/Phenix communication APIs.
• Implement fragment extension ChimeraX user interface.
• Implement ligand placement ChimeraX user interface.
• Implement restraint specification ChimeraX user interface.
• Implement validation ChimeraX user interface.

CZI Essential Open Source Software August 2021-2023 - Molecular Visualization: Transitioning Chimera to ChimeraX

Plan

• Export Chimera sessions to ChimeraX.
• Port multiple sequence alignment and homology modeling web services.
• Update the Qt window toolkit from version 5 to 6.
• Replace OpenGL graphics with Vulkan.
• Distribute a native ChimeraX for Mac ARM CPUs.
• Develop a PyPi library to distribute non-UI components of ChimeraX.

Completed

R01 July 2018-2022 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling

Plan and aims and ​NIH Reporter

• Aim 1: Interactive visualization and analysis platform (ChimeraX)
  • 1A: Support very large homogeneous and heterogeneous data sets
  • 1B: Integrate visualization of non-spatial 2D data with 3D graphics
  • 1C: Implement novel analysis and modeling tools
  • 1D: Export ChimeraX data for web-based visualization
• Aim 2: Atomic resolution modeling from cryo-electron microscopy datasets
  • 2A: Develop analyses of map quality for model building
  • 2B: Create interactive model building and measurement tools
  • 2C: Devise new model validation tools
• Aim 3: Community development platform for new algorithms and methods
  • 3A: Create and document APIs for ChimeraX libraries
  • 3B: Design and implement web-based ChimeraX bundle repository
  • 3C: Develop bundle contribution method for community developers

NIAID contract, March 2021 - 2022

Plan

• General ChimeraX improvements to support NIAID (Eric: 20%)
• Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development. (Eric: 15%)
• Improve multi-person VR (Tom: 35%)
• Human Biomolecular Atlas Program (HuBMAP) multiscale visualization (Eric: 30%)
• Enhance ChimeraX’s segmentation capabilities (Tom 40%)
• DICOM (Tom: 25%, Eric: 5%)
• Outreach - Instructional material and tools documentation (Elaine 20%)
• Administration (Scooter 10%)