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/cagebuilder.html>

* 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,