Chimera Next Generation

Tom Goddard
June 3, 2013
Group meeting

What will make people want to use Chimera 2?

• New features.
• Better user interface.
• Better performance (speed, reliability).

This presentation will discuss my experiments of the last few months to what these improvements might look like.

Updating the sofware we use

Observations about new software libraries:

• Qt has more features than Tk, for example HTML display.
• Qt is as buggy as Tk, encountered 7 significant bugs so far.
• Python 3 about the same as Python 2, no difficulties.
• OpenGL 3 core profile, cleaner, simpler, and more flexible than OpenGL 1 and 2.
• OpenGL all handled from Python (PyOpenGL) -- no performance problems so far because data is passed in large arrays with few function calls. Faster to debug and develop than OpenGL in C++.

Demonstration

Mostly I have tried user interface experiments, with several HTML interfaces. Molecule speed and memory use is 10-100x better than Chimera 1. No improvement for density maps. Have not tried any new features. A possible direction: comparing hundreds of PDB models.

Demonstration Details

1. Recent sessions icons. Startup shows session icons using HTML, scrollable, wrapping - resize window to show this.
2. Fit molecule in map example, open 1grl_fit session.
3. Move molecule mouse mode. Show positioning molecule for fit.
4. Find model numbers for fit command. Tiled model display.
5. Command: fit #2 #1
6. Contour level mouse mode. Make map surface larger to assess fit better.
7. Make map transparent. Ice cube toolbar icon. Shows single layer transparency.
8. Show simulated map to compare fit. Command "molmap #2 10".
9. Change original map color to gray. "volume #1 color gray style mesh".
10. Make sim map transparent. Selection mouse mode, select it. Ice cube icon to make transparent.
11. Show tiled 3 models.
12. Show save session toolbar icon and save dialog.
13. Reply log with images. Can have links, thumbnails as scenes, repeat commands. Show grant proposal log example.
14. Now show some high performance examples.
15. Autopack HIV model (surface GPU instancing, where Chimera 1 uses slower CPU instancing).
16. Show tiled models. Hide spikes and matrix protein. Hide tiles.
17. Reovirus biological unit, molecule instancing. Chimera 1 cannot do molecule instancing.
18. Shortcut st (stats), 2 million atoms.
19. Open 188 HIV reverse transcriptase models. Chimera 1 movie took a day to make. High memory use (10 Gbytes), extremely slow. High performance will allow Chimera 2 to do comparisons of many structures.
20. Open 188 HIV RT models. Use command log (html, links). Loads in ~5 seconds, 380 Mbytes total Chimera size.
21. Next want to align, show ribbon, recreate movie in a few easy steps.
22. Manual. HTML in app. Browse to fitmap subsection and back to index with back button.
23. Keyboard shortcut help.
24. Leap motion chopstick interface. Show visualizer, explain stereo cameras track 10 fingers. Might show advertising trailer, then demo my code.

Grant Proposal Example Command Log

Leap Motion Controller

• Wave hands to control your computer. Show trailer.
• Input device with two cameras tracks positions of ten fingers.
• Show Chimera 2 chopstick leap motion interface.
  • Move fingers apart to zoom in.
  • Move fingers in same direction to translate.
  • Move fingers around a center point to rotate.

Next Steps

• Align and ribbon for HIV 188 structure comparison.
• Use GIT code repository.
• Port more density map and surface commands.
• Use list panel (maybe html) below graphics for map fits, view dock results, model list.