[Chimera-users] 1.2251 snapshot release

[Eric Pettersen]

Hi all,
	There is a new snapshot release (1.2251) available, with a potpourri  
of new features, listed below.  The release is for all platforms, but  
on Mac we had a little difficulty getting things to work for OS X  
10.3, so this release is 10.4 only, but the next production release  
will include 10.3 support.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu
---
1.2251 release (changes since 1.2199 release)

GENERAL:

Session files are smaller, use less memory, and start faster.

CIF/mmCIF files can be read (or fetched by ID from RCSB)

Electron density maps can be fetched by PDB ID from Electron Density  
Server

Virus Particle Explorer (VIPER) files can be fetched by ID

VIPER input automatically starts Multiscale Models and constructs  
viral capsid

Thinner default ribbons

Files opened by scripts (either Python or Chimera commands) are now
   searched for relative to the script location, not Chimera's  
startup location.

Can switch to sequential stereo mid-session without having used --stereo
    at startup (except on certain Windows systems)

New stereo mode: anaglyph (offset red/cyan-tinged views, like 3D movies)


NEW TOOLS:

Add Charge (Structure Editing) -  assigns partial charges to atoms;
    Amber (Cornell et al. 1995) charges used for standard residues,
    Amber's Antechamber module (now included with Chimera) used to
    calculate charges for nonstandard residues

Build Structure (Structure Editing) - under construction but basic  
functions work;
   not much documentation

ReadStdin (Utilities) - allows communication with Chimera through  
standard input/output


TOOL CHANGES:

AddH (Structure Editing)
   - new options including how to treat histidines

Adjust Torsions (Structure Editing)
   - interface reorganized to show atoms defining a torsion in order  
1-2-3-4
   - options added to control decimal places and show degree symbol  
in angle labels

Dock Prep (moved to Structure Editing)
   - option added to delete alternate locations of atoms
   - hydrogen addition and charge addition details split off into  
separate tools
       called from Dock Prep (AddH and Add Charge, respectively)
   - terminal carboxylates/amines completed as appropriate

Effects (Viewing Controls)
   - background transparency option added
       (previously only available as --bgopacity startup option)

Minrms Plot (Structure Comparison)
   - Show Alignment option added

MPOSE extension removed (Structure Comparison)

Multalign Viewer (Structure Comparison)
   - .ali extension interpreted as PIR format
   - .pfam extension no longer indicates Stockholm format, instead  
indicates Pfam format
       ("Plain Pfam format" at the Sanger Institute Pfam site)
   - changed default residue letter/region colors for improved  
readability
   - improved editing response time
   - editing no longer pushes residues that are not in the active region
   - added control over whether a region depiction spans gaps
   - option to associate a structure chain with the best-matching  
sequence in the alignment
       (when criteria for automatic association are not met)
   - new Edit menu allowing sequence reordering and deletion, gap  
column addition and deletion


COMMAND CHANGES:

ribbonjr removed


NEW COMMANDS:

addcharge - assign partial charges to atoms
   (command-line implementation of new Add Charge tool)

intersurf - generate and display interface surfaces
   (command-line implementation of Intersurf)

setattr - set a new or existing attribute to a specified value

surftransparency - adjust molecular surface transparency

COMMAND CHANGES:

longbond - now takes an atom or model specification to restrict the  
calculation
   to certain models

TUTORIALS:

figures added to Getting Started tutorials

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