UCSF Chimera Release 1.5

Release timeframe: January 2010

Possible 1.5 features

1. Mouse modes palette. TG
2. Implement mmcif template web service to update templates dynamically from chimera
3. Allow sending template structure and template/target sequence alignment to comparative modeling program, either local or Web. ECM
   • This will require discussion/clarification between Andre and Tom to align the research goals of the two groups
4. 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
5. Higher quality lighting and transparency using OpenGL shaders. TG
   • Maybe discussed in conjunction with a more complete discussion about improving scenegraphs
6. Color tint/fade capability (modulate instead of replacing current colors). Further investigation suggests the desired effect might be attained by making it easier to adjust transparency without otherwise changing the current coloring scheme, as is already available for surfaces (but not ribbons, atoms, objects)... but probably transparency would itself need to be improved. ECM
7. 2D Labels: individual label show/hide capability so that you don't have to make separate sessions for images that are just different views of the same thing. ECM
8. 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
9. 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).
10. 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
11. Display preset wizard. EFP
12. Python 2.6 GC
    • wrappy changes
    • allows for 64-bit Windows builds (needs Microsoft Visual Studio 2008)
13. Improve VRML by making nodes into Python objects and selectable geometry GC
14. Bring OSMesa version to production status GC
    • split test suite into gui and non-gui parts
    • add tutorial
15. Benchmark graphics options (multisampling, bgopacity) GC
16. Add more types of dashed lines in POV-Ray/Renderman GC
17. N-level transparency without sorting using depth-peeling GC
18. Web distribution of extensions CH
19. Remove OTF. TG
20. Distinguish real molecules from marker models and other non-molecular uses of Molecule class. This could involve a flag to indicate a Molecule instance is non-chemical, or a new Graph base class of Molecule. TG

Features Postponed to 1.5+

These features will be re-evaluated for the 1.5 release, but we think they are likely to be postponed beyond that.

1. EMANimator++ EFP
   • Tom and Wau will look for additional funding to support this
2. Tool configuration wizard. EFP