General:
- File menu includes Save PDB
- Fetch by ID is a separate entry in the File menu and a separate dialog (was previously combined with the File Open dialog); NDB IDs can be used here and in the command line, e.g., ndb:tr0001
- default "all atom" VDW radii are now based on Amber parm99
- labels are now automatically offset in viewing coordinate system instead of the model coordinate system and thus are always to the right of atoms and always in front of bonds. Label offsets can only be adjusted programatically in this release
- More accelerators (keyboard shortcuts)
- moved C3' off ribbon backbone so sugar isn't distorted
- support added for NurbsCurve and NurbsSurface VRML nodes
- initial OpenGL Shading Language API support
New Tools:
- Define Attribute (Utilities, Programming) — assign values for new or existing attributes to atoms, residues, or models
- Nucleotides (Graphics) — create special nucleotide-specific displays, including VRML representations of the base and sugar moieties
Tool Changes:
- AddH improved to avoid clashes; added to functions in Model Panel
- Color Secondary Structure has Defaults button (restores color wells to default colors)
- Demos can be saved from the menu; can be enclosed in chimerax files; demo.src AUTORUN_ON tag added; Cancel no longer closes models that were already open when a demo was started; many HTML-type tags can be used in the text sections
- Lens Inspector has more options for atom labeling
- Match -> Align uses an improved algorithm for multiple alignments, which can handle circular permutation
- Movie can read PSF/DCD files from CHARMM, NAMD, X-PLOR; can read PDB-format trajectories (single concatenated file or one file per frame)
- Multalign Viewer can save an alignment subset (the active region) to a file; an alignment saved in Stockholm format automatically includes annotations describing the secondary structure of any associated structures
- Multiscale Models includes the zone selection options Near and Contacts
- PipesAndPlanks now connects the secondary structure elements with loops
- Preferences can be reset/restored/saved for an individual category (previously only for all categories at once); Web Data category renamed "Web Access" and includes HTTP proxy options; label font/size moved from General category to Background category
- Rainbow GUI is in the Graphics Tools (previously only accessible from the Model Panel), has Defaults button to restore color wells to default colors
- Render by Attribute includes Radii section (atom radius scales with attribute value) and Worms section (worm radius scales with attribute value)
- Ribbon Style Editor scalings are now analogous to cross sections (per-residue, no startup default except in New Molecules Preferences); new "residue class" section allows specification of which atoms should guide the ribbon path, thus generalizing ribbons to polymers other than standard peptides and nucleic acids
- SimpleSession saves custom coloring of molecular surfaces, aliases
- ViewDock includes new interface for choosing compounds by descriptor values
New Commands:
- addaa — add amino acid residues to the C-terminus of a peptide/protein
- addh — add hydrogens (command implementation of AddH)
- bond/~bond — create and delete bonds
- chirality — report the R/S configuration of a chiral center(see User's Guide for caveats)
- defattr — define a new attribute and/or assign attribute values
(command implementation of Define Attribute)- rangecolor — color over a range according to attribute values
- rmsd — evaluate the RMSD between specified sets of atoms (without matching)
Command Changes:
- a command is not automatically erased after execution, but generally the text remains highlighted so that the next command replaces it rather than being appended to it
- atom specification operators added for union (|) and negation (~) (previously just intersection (&) and operators for combining attributes only)
- "fromeditor" synonym for "colorpanel" and "byelement" synonym for "byatom" in coloring commands
- hbonds has "tilde version" ~hbonds, which removes the pseudobonds showing hydrogen bonds
- labelopt info has "res" or "residue" keyword indicating that only residue name and number should be shown (not atom name)
- rainbow can color by model (previously only by residue or chain); likewise for the rainbow GUI opened from the Model Panel
- select has "up" and "down" arguments which behave like up arrow and down arrow to broaden and narrow a pre-existing selection
Tutorial Changes:
- Images for Publication tutorial updated because PDB entry 1uyp replaced 1utw