Attendees

Conrad, Elaine, TomG, Greg, Eric, Scooter, TomF

Agenda

• Demo by TomG of CRISPR, Ribosome and NPC structures as examples of complex assemblies (see ​Data hierarchy and groupings slide
• Discuss what entities are necessary and what their relationships are

Discussion

• List of basic entities:
  • Assembly
  • Volume
  • Protein
  • Nucleic Acid
  • Chain
  • Domain
  • Helix
  • Sheet
  • Solvent
  • Ion
  • Metal
  • Crosslink (aka pseudo-bond)
  • H-bond
  • Missing segment

• List of computed, predefined, or user defined entities/groups
  • Surface
  • Active Site
  • Axes
  • Centroid
  • Planes
  • Ellipsoids

• Hierarchical relationships:
  • Assembly
    • Chain
      • Domain
      • Helix$
      • Strand$
      • Sheet$
      • Missing Segment
      • <Sequence>
      • *Any computed/predefined/user-defined item
    • Protein$
    • Nucleic Acid$
    • Ligand$
    • Ion/Metal$
    • Solvent$
    • Crosslinks
    • H-bonds
    • Volume
    • Sheet
    • Coarse Grained Model
    • Assembly
    • *Any computed/predefined/user-defined item
  • $ = ChimeraX-defined groups

Action items

• Continue discussion at next CDM