Hello everybody, A new production release of UCSF Chimera (version 1.6) is available: <http://www.cgl.ucsf.edu/chimera/download.html> Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). This will be the last Chimera release supporting Mac PowerPC platforms and OS X 10.5 (Leopard). New features include a Rapid Access interface to frequently used data and tools, new ribbon spline options, improved transparency rendering, new fetch type: Uniprot protein sequence and annotations, and several options for fitting atomic structures into density maps: global search, iterative sequential fitting, symmetric fitting, etc. More details are given below; see release notes for the full list: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html> Graphics, Depiction: * new spline options for ribbon closer to backbone atom positions * new initial model colors, pastel rather than saturated * improved transparency rendering (global single-layer on by default) * 3D labels drawn on top by default * fancy backgrounds: images from files, color gradients from Palette Editor * options for cleaner pocket/tunnel surface display (see "sop" command) Structure Analysis and Modeling: * AddH allows specifying less common states of Asp, Glu, Lys, Cys * FindHBond can label H-bonds with distances * Blast Protein shows more info for PDB hits (ligands, resolution, etc.) * Build Structure improvements for joining peptides, swapping substituents * tools to change chain IDs, renumber residues * minimization: - can be conjugate gradient (previously steepest descent only) - parts of structures can be ignored * distance and angle plotting for trajectories * Cage Builder tool for generating polyhedral cage models <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebui...
* interface to MultiFit web service (simultaneous rigid fitting of multiple structures to density, developed by the Sali Lab, UCSF) * "fitmap" command: - global search with random initial placement - iterative sequential fitting - symmetric fitting * "measure" command options: - map symmetry - surface contact area - center of mass User Interface and I/O: * Rapid Access interface to frequently used data and tools shown at startup, can be hidden/shown at any time by clicking the lightning-bolt icon <http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html> * caching fetched data is turned on by default * scaling with mouse/touchpad scrolling can be turned off (Mouse prefs) * Model Panel: - group/ungroup function, such as for NMR ensembles - functions reorganized into favorites/all * new input types: SPHGEN spheres, Maestro/Glide docking output (ViewDock) * WebGL export (experimental feature) Sequence-related: * new fetch type UniProt: protein sequence and feature annotations * Multalign Viewer: - UniProt features can be mapped onto already open sequences - Region Browser improvements for handling feature annotation regions - calculation of region overall RMSD - interface to Modeller homology modeling allows including water, other HET Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu