Possible Core Features for a Future Chimera Release

1. Pull mmcif connectivity information from a web service. The current mmcif connectivity template file is 20MB uncompressed and constantly out of date. Rather than including the file in our release, the proposal is to include only the most common entries and pull the rest from a web service, as needed. Entries will be cached once they are downloaded, and the user will be able to download the entire file, should they desire.
2. CMS Surface code.
3. 64-bit Mac Aqua build for large volume data applications. TG
   • We had discussed having this happen when OS X 10.6 (Snow Leopard) comes out. It's supposedly slated for Q1 2009. EFP
4. Higher quality lighting and transparency using OpenGL shaders. TG
   • I guess these would be options in the Effects panel; need "effects" command for controlling all Effects (not just these new things) via script. ECM
5. Off-screen image saving (using opengl write-to-texture?) so machine does not become unusable during animation encoding. TG
6. Replace mac aqua focus-follows-mouse with click-through. Tk patch probably required. TG
7. Record usage statistics, submit with registration. TG
8. Output compressed TIFF instead of current giant files. ECM
9. Color tint/fade capability (modulate instead of replacing current colors). ECM
10. Provide our own Web services for BLAST on PDB, multiple sequence alignment (ties in with Core 4). ECM
11. Interface with comparative modeling software (ties in with Core 4). ECM
12. BILD and/or shape command ability to create ellipsoids. ECM
13. Nucleotides: saved in sessions, dialog settings maybe sticky, "nucleotides" command, possibly use in preset. ECM
14. MD Movie: checkbox in Per-Frame panel and/or Record Movie panel to recompute secondary structure (make it more obvious that ribbon display may need to be updated). ECM
15. Build Structure: allow bonding of one clump of atoms to another clump of atoms in a way that automatically repositions one clump instead of requiring the user to attempt to maneuver it into the appropriate bonding position. ECM
16. Minimize Structure: don't call Dock Prep again if all atoms already have amberType and topology has not changed. ECM
17. Read PDBPQR format and load charge and radius values as the respective attributes. ECM
    • Perhaps write PDBPQR format.
    • Perhaps read PDBQT (Autodock format) and load charge, autodockType (or something like that).
18. Make it easier to get phi,psi,omega,chi torsion values from proteins. Maybe a button on Angles/Torsions to assign the values as residue attributes?
    • Longer term, interactive Ramachandran plot. ECM
19. Reposition normal labels with mouse. EFP
20. Display multiple trajectory frames simultaneously. EFP
21. Trajectory smoothing. EFP
22. Trajectory analysis timeline plots. EFP
23. EMANimator++ EFP
24. Tool configuration wizard. EFP
25. Display preset wizard. EFP
26. (planned/probable) Measure planes/centroids. EFP
27. (planned/probable) Rename models using Model Panel. EFP
28. (planned/probable) Coulombic surface coloring. EFP
    • Elaine would like it to generate a map.
29. (planned/probable) Finish Color Key (X3D output [needed for raytracing]; "key" option to rangecolor command). EFP
30. integrate Nucleotides GC
    • session support, command line, rings filling per residue, 2D representation, interpolating ribbons GC
31. move Molecule color to Model GC
32. Python 2.6 GC
    • wrappy changes
    • allows for 64-bit Windows builds (needs Microsoft Visual Studio 2008)
33. off-screen rendering GC
    • improve shadow resolution GC
34. Improve VRML by making nodes into Python objects and selectable geometry GC
35. X3D import GC
36. NURB ribbons GC
37. Bring OSMesa version to production status GC
    • split test suite into gui and non-gui parts
    • add tutorial
38. Benchmark graphics options (multisampling, bgopacity) GC
39. Support additional fonts GC
40. Add more types of dashed lines in POV-Ray/Renderman GC
41. N-level transparency without sorting using depth-peeling GC
42. Web update without reinstall CH
43. Web distribution of extensions CH
44. Framework for invoking chimeraservices.rbvi.ucsf.edu CH
    • Security, transactions with IDs
45. Animation interface (same as EMANimator++?) CH
46. General grouping mechanism for domains, quaternary structures, regions, etc. (probably not for 1.4)
47. Improvements to lighting panel user interface. The idea is to make the most commonly useful light controls more accessible. Have the "lights (basic)" panel contain the current brightness slider, move key-to-fill ratio to advanced, add one shininess slider which simultaneously makes specular highlights brighter and smaller (the advanced interface would let you control spot size and brightness independently), have the glossy/normal setting. Move the shininess pane controls to advanced, renaming brightness and shininess to avoid confusion. Move the naming and using of default settings to a new pane in the lights (basic), lights (advanced) menu called "named settings". This will free up some extra vertical space for the added advanced options. TG
48. Use numpy for vector, point, transform, bounding box, coordinate set data types. Our current home-brewed Vector, Point, and Xform classes are a significant obstacle to implementing geometric calculations. The Chimera volume data code is littered with conversions back and forth between these undernourished data types and the much more usable numpy arrays. TG