[Chimera-users] new Chimera production release

[Eric Pettersen]

Hi all,
	A new Chimera production release (version 1.1951) is now available for 
download.  I've summarized the major additions since the last snapshot 
(1.1917) below.  A list of all the changes since the last production 
release (1.1872) is in the release notes:  
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.1951.html

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu

Changes since 1.1917:

General changes
---------------

Newly opened models are shown larger (as well as models after a 
'window' or 'focus' command)

Selections can be written out as parsable text files (Actions->Write... 
or from the Selection Inspector)

New residue attributes:
     kdHydrophobicity (Kyte-Doolittle hydropathy, amino acids only)
     mavPercentConserved (% conserved in a sequence alignment open in 
Multalign Viewer)
above for use with Render/Select by attribute tools

Double-picking a bond brings up a menu with Rotate Bond and Select 
Bonded (the latter is new and selects the atoms); double-picking a 
pseudobond bring up a menu with just Select Bonded; "select bonded" 
also now in Pseudobond Panel

As much as possible, can handle PDB files with 100000+ atoms (e.g. 
AMBER output).  Some PDB records (e.g. CONECT records) have no room for 
6-digit atom serial numbers, so only can be used for the first 99,999 
atoms.

A new tutorial describing preparing images for publication

Select by Attribute Value... in Selection menu and Model Panel


New Tools
---------

Lighting (Viewing Parameters): change and save lighting parameters

Color Secondary Structure (Graphics): color peptides/proteins by 
secondary structure

Render Attributes (Graphics):  color or otherwise change atom, residue, 
or model displays based on attribute values;  was in 1.1917 release but 
several changes have been made and documentation added

Demo (its own category; entries are individual demos):  create/replay 
demos in Chimera; example demo included (Cyclooxygenase)


Tool Changes
------------

Adjust Torsions now allows a bond to be rotated with mouse motions in 
the graphics window

Movie has File->Save PDB for writing out either the current frame or 
all frames that have been viewed

Multalign Viewer:  ClustalX-style residue letter coloring added and 
made the default; can save alignment depiction as an EPS file; can hide 
Consensus and/or Conservation lines

RibbonStyleEditor now has two panels in which scalings and 
cross-sections can be defined and named; named cross-section are 
analogous to the built-in cross-sections (flat, edged, round) and can 
be accessed from the Actions menu or with ribrepr; nucleic acids are 
now treated separately in the scalings panel

New "Graphics" category; Per-Model Clipping, PipesAndPlanks, ResProp, 
and Ribbon Style Editor moved into it

SimpleSession saves lighting, ribbon scaling and cross-section(s), 
B-factor and occupancy values

Web Data asks for confirmation before accepting certain files; 
associated option in Preferences


Command Changes
---------------

alias: $1, $2, $3, ... may be used to indicate the first, second, 
third... arguments of the alias

conic: works on Windows, and the -s flag now works on Linux (besides 
Mac, SGI)

write: has "trajectory" keyword to write all frames that have been 
viewed (loaded) [analogous option added to Model Panel's "write PDB" 
dialog]

ribbackbone: now applies to nucleic acids also