[Chimera-users] 1.9 production release

Eric Pettersen pett at cgl.ucsf.edu
Tue May 13 12:36:04 PDT 2014

Hello everybody,
A new production release of UCSF Chimera (version 1.9) is available:

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).

New features include multiple sequence alignment using Clustal Omega
or MUSCLE web services, building double-helical nucleic acids,
"colorkey" command, "struts" command to reinforce structures for
3D printing, "vseries" volume series playback and processing options,
more efficient save/restore of coordinates in sessions, Dynameomics 
amino acid rotamer library, WMV2 movie output, COLLADA export.

More details are given below; see release notes for the full list:

Display, Interface:
* icon for menu selection mode: Append, Intersect, Replace, Subtract
* distance monitor line style and color can be saved as preferences
* silhouette outlines can be controlled per-model 
* Axes/Planes/Centroids objects can be recolored with Actions menu
* "colorkey" command implementation of Color Key tool

Structure Analysis and Modeling:
* new Align Chain Sequences tool for multiple sequence alignment of
structure chains using a Clustal Omega or MUSCLE web service
(these can also be called to realign the sequences in an existing
Multalign Viewer window)
* "mda" command to Blast-search and retrieve structures similar to
a query sequence, lay them out left->right by N->C along the query
* APBS interface omits explicit solvent by default
* "coulombic" command allows specifying atoms/charges to use for ESP
calculation independent of the surface to color
* Build Structure tool allows generating nucleic acid double helices,
specifying phi angle when joining peptides
* "adjust" command to change bond angle or length
* MD Movie session support for partly loaded trajectories
* Morph Conformations pairs chains by ID if the sets of IDs are same
* "ramachandran" command can assign probabilities as attributes
* Rotamers/swapaa include Dynameomics rotamer library (Daggett group)

Volume Data (density maps, ESP maps):
* "vop" volume operations to take pointwise maximum or multiply maps
* "vseries" command options to open and close volume time series,
jump playback to a specific frame, perform various processing such
as alignment, normalization, cropping, compressing, save to file
* new volume input format VTK structured points (ASCII)

General, I/O:
* some Preferences reorganization, new categories: Labels, Selection
* more efficient save/restore of coordinates in sessions
* new output movie format WMV2
* new export formats COLLADA, VTK
* "struts" command to add strengthening bonds for 3D printing
* "leap" command for using Chimera with a Leap Motion Controller

Enjoy! On behalf of the Chimera team,


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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