Hi all, A new Chimera snapshot release (version 1.2029) is now available for download. I've summarized the major changes since the last release (1.1951) below. A list of _all_ the changes since the last release is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2029.html Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu General changes --------------- The "web fetch" part of the "File...Open" dialog has been split off into its own "Fetch by ID" dialog. The Fetch dialog now supports fetching NDB IDs. Labels are now offset in the viewing coordinate system (rather than the model coordinate system), making them much less likely to be obscured. Moved C3' off of ribbon backbone so that the sugar ring isn't distorted. New Tools --------- Nucleotides (Graphics): create various nucleotide-specific depictions, such as stylized representations of base pairings or filled sugar rings Define Attribute (Utilities, Programming): assign values to new or existing attributes of atoms, residues, or models. Particularly useful in conjunction with the Render by Attribute tool. Tool Changes ------------ AddH improved to avoid steric clashes (and appears in model panel) Match -> Align can handle circular permutations in multiple alignments [formerly only in pairwise] Movie can read PSF/DCD files from CHARMM, NAMD, and X-PLOR; can read PDB-format trajectories (single concatenated file or one file per frame) Multalign Viewer can save a subset of an alignment to a file Multiscale Models includes the zone-selection options Near and Contacts PipesAndPlanks now connects the secondary structure elements with loops Web Data preference category renamed to Web Access and includes HTTP proxy options Render by Attribute implements Radii section (atom radius scales with attribute value) and Worms section ("worm" ribbon radius scales with attribute value) Ribbon Style Editor scalings are now treated similarly to cross sections (per-residue, no startup default except in New Molecules preferences); new "residue class" tab allows specification of which atoms should guide the ribbon, this generalizing ribbons to polymers other than standard peptides and nucleic acids ViewDock includes new interface for choosing compounds by descriptor values New Commands ------------ addaa: add amino acids 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 --------------- atom specification operators added for union (|) and negation (~) [previously just intersection (&) and operators for combining attributes] 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 Rainbow tool select has "up" or "down" arguments which behave like up-arrow and down-arrow to broaden and narrow a pre-existing selection