General:
- uses new PDB web interface for fetching PDB files (older chimera's will fail starting sometime after June 2006)
- can write out Mol2 files (File... Save Mol2)
- new input format, BILD: simple descriptions of lines, polygons, and basic geometric forms are used to make a VRML model in Chimera (was available earlier but mostly undocumented)
- new format for atomic coordinates: XYZ
- new volume formats: Gaussian cube grid, Purdue image format, Situs map file
New Tools:
- Angles/Torsions (Structure Analysis) — table of angle monitors, analogous to the Distances panel
- Dock Prep (Surface Binding/Analysis) — perform several tasks to prepare structures for use with DOCK (or other programs): delete solvent, add hydrogens, load charges, write as Mol2
- Fit Models in Maps (Volume Data) — locally optimize the fit of a structure within a density map
- Icosahedron Surface (Higher-Order Structure) — create a hybrid icosahedron/sphere surface
- Intersurf (Surface Binding/Analysis) — generate and display interface surfaces (was available earlier but undocumented)
- Measure Volume (Volume Data) — measure the volume enclosed in a surface
- Set Bond Length (Structure Editing) — set lengths of selected bonds arbitrarily
- Volume Eraser (Volume Data) — interactively zero out parts of volume data
Tool Changes:
- AddH (moved to Structure Editing) — deletes lone pairs and unidentifiable-element atoms; uses Amber parm99 bond lengths for X-H (X=C/N/O/S)
- Adjust Torsions also moved to Structure Editing category
- Color Zone (Volume Data) — colors to match the closest atom rather than any atom within the cutoff
- Effects (Viewing Controls) — silhouette edges can be drawn to highlight borders and discontinuities
- Match->Align (Structure Comparison) — default cutoff 5.0 angstroms
- MatchMaker (Structure Comparison) — default iteration cutoff 2.0 angstroms; added option to calculate secondary structure assignments prior to matching (on by default)
- Multalign Viewer (Structure Comparison) — Ctrl-arrow editing shifts the active region rather than the last-drawn; gap columns can be added on the ends; Copy/Rename buttons on Region Browser; percent identity calculation (Tools... Percent Identity); can load custom residue letter coloring schemes (Tools... Load Color Scheme); Structure Match default iteration cutoff 2.0 angstroms
- Multiscale Models (Higher-Order Structure) — setting Resolution to 0 triggers calculation of solvent-excluded molecular surface instead of the usual low-resolution surface
- Surface Color (Volume Data) — can use up to 20 colors (previously 5); can use preset rainbow, grayscale, and red-white-blue color patterns
New Tutorial:
- Trajectory and Ensemble Analysis
- other tutorials updated
Major Bugs Fixed:
- eliminated several memory leaks (some remain in third-party code)
- off-by-one MD Movie/recording fixed
- transforms in BILD format now work correctly
Known Bugs:
- POV-ray output is missing boxes and cones, so Nucleotide representations are not visible. The workaround is to use RenderMan output and a RenderMan renderer, like the freely available one from 3delight. This is fixed in the next release.
- On Windows, the POV-ray and RenderMan exporters fail due to a missing dll. The fix is to copy CHIMERA/bin/zlib.dll to CHIMERA/bin/zlib1.dll so that both exist. This is also fixed in the next release.
- bond rotations in large molecules are slow
- ribbon transparency doesn't work correctly on all platforms
- cross-eye stereo parallax is wrong
- surfaces fail for some structures