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 ​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