User Functionality

What areas of functionality should be in a Chimera 2 initial release?

What productive work will users do more easily than with Chimera 1?

Should an initial release support one or two functional areas in depth, or broad areas with shallow coverage?

There is a ​list of ideas in Hydra feature slides from March 2014.

Areas. Can we make these significantly better than in Chimera 1?

• Scenes
• Presentation images (ribbons, pipes planks, nucleotides, surface capping, pseudobonds)
• Animations (timeline gui with more automatic transitions, commands with frames options, morphing)
• cellPACK / multiscale models (opening data, grouping, clipping, running cellPACK, cage builder, symmetry copies)
• Multi-Domain Assembler (port?)
• Comparitive structure analysis (match maker, morphing, tiling, clustering, showing differences)
• Single sequences, interactive display, secondary structure, database annotations
• Sequence alignments
• Structure build/refine (addH, loop model, homology model, minimize, swapaa, build standard geom, symmetric copies)
• Optical microscopy 3d time series
• Cross-links and EM, Jan Kosinski EMBL, IMP, Rosetta
• Protein-protein interfaces (clashes, electrostatic potential, add charge, hydrogen bonds, nice contact map depictions)
• Measurements, rmsd/axes/planes/centroids/angles/distances/buried area/cavity volumes/symmetry with graphical depictions.
• Docking results analysis, ViewDock
• Small ligand binding analysis (zones, pocket surfaces, areas, hydrogen bonds, metal coordination, electrostatics...)
• Evaluating models in high res (3A) EM maps
• Map fitting
• Map segmentation, Segger
• Molecular dynamics (md viewer, solvate, add ions, md simulation)
• Demo capability, use html, for teaching