Chimera 2 Density Map Progress

Tom Goddard
May 2, 2013

• Using Qt 5, PyQt, OpenGL 3.2 core profile, PyOpenGL, Numpy, Python 3.3
• Open maps, surface/mesh/grayscale/orthoplanes/box/outlines display.
• Mouse modes to adjust contour levels, resize volume, move planes, move molecules.
• Molecules sphere style, opengl instancing, color by chain or atom, biological unit.
• Fast molecule load, 0.5 seconds for 400,000 atom 2 ribosomes 3u5* (8 files). 25 seconds in Chimera 1, 15x less memory use.
• Fit molecules in maps.
• Save sessions, session thumbnails (textures on surfaces), session history, sessions contain data only.
• Save images (no supersampling).
• Camera view matrix for rotation, translation, zoom.
• Keyboard shortcuts, open/save dialogs.
• Density map C++ code all in one library (e.g. interpolation, histogram calc, ...).
• Python interface to C++ hand coded.
• Not using Chimera 1 opengl code, _chimera core library, wrappy, _molecule library.

Observations

• Much of Chimera 1 core _chimera.so could be in Python.
• OpenGL 3 can be done in Python -- few calls operating on arrays.
• Overlays in graphics is simpler user interface.

Things to try

• Try selection highlighting by dimming all unselected models.
• Try tiled display of all models for showing and hiding and other model panel actions.
• Add column of mouse mode buttons in main window.
• Use Sphinx for documenting APIs.
• Add volume histogram graphics overlay.
• Side view and lighting could be graphics overlays.
• Fly through animation with new camera interpolation.
• Map display from asymmetric unit for large EMDB maps.

Things to port

• AutoPack surface models.
• Surface clipping and capping.
• Surface coloring (radial, electrostatics, ...).
• Marker placement.

Direction

• What new features can make Chimera 2 enticing to users?
• What user interface improvements can make Chimera 2 enticing to users?
• What demonstrations of Chimera 2 will help sell it?