[Chimera-users] new Chimera snapshot release

[Eric Pettersen]

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