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 programmatically in this release
- more accelerators (keyboard shortcuts)
- moved C3' off ribbon backbone so sugar isn't distorted
- dialog for custom residue labeling (Actions→Label→residue→custom...)
- 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 and also appears in the Graphics category (previously just Inspectors)
- 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
- Per-Model Clipping allows a clipping plane to be flipped 180 degrees and/or aligned with that of another model
- 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
Major Bugs Fixed:
- ~color command now respects b l v s specifiers
- fixed SideView bounds to match perspective frustum
- Phantom 6-DOF input device support updated for IRIX and Windows
- Collaboratory now transmits surface transparency
- non-orthonormal rotation matrices no longer sneak in
- VRML IndexedFaceSet now works when no colors are given
- lens outlines now appear in saved images
- residue names that start with digits are no longer treated as positions
- handle backslashes in filenames better (esp. Windows)
- don't overwrite old session if session save fails
Known Bugs:
- on Windows, tools that generate VRML models (e.g. Nucleotides, Pipes and Planks) might fail if they can't write to the root directory of the current drive — fixed in the 1.XXXX snapshot
- MatchMaker's second chain-pairing option ("specific reference chain with best-aliging chain in match structure") is broken
- volume rendering doesn't work correctly on Mac OS X before 10.3
- The "save H-bonds to file" option of the FindHBond tool is broken. A workaround is to use the command-line "hbond" command instead.
- ribbon transparency doesn't work correctly
- cross-eye stereo parallax is wrong
- bond rotations in large molecules are slow