= User Functionality =

What initial areas of Chimera 2 functionality should we develop to allow users to do productive work more easily than with Chimera 1?

There is a [http://www.cgl.ucsf.edu/chimera/data/hydra-mar2014/hydra.html#ideas list of deas] in Hydra feature slides from March 2014.

Areas.  Can we make these significantly better than in Chimera 1?  Which are best for an initial release?

 * Scenes
 * Presentation images (ribbons, pipes planks, nucleotides, surface capping, pseudobonds)
 * cellPACK / multiscale models (opening data, grouping, clipping, running cellPACK)
 * 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)
 * 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, axes/planes/centroids/angles/distances/buried area/cavity volumes with graphical depictions.
 * Docking results analysis, !ViewDock
 * Small ligand binding analysis (pocket surfaces, areas, hydrogen bonds, metal coordination, electrostatics...)
 * Evaluating 3A EM maps and atomic models
 * Map fitting
 * Map segmentation, Segger
 * Molecular dynamics (md viewer, solvate, add ions, md simulation)
 * Demo capability, use html, for teaching