[Chimera-users] new Chimera snapshot release

[Charles Moad]

The release notes include: initial OpenGL Shading Language API support.

Do you have any documentation on how you expose this functionality, or
could you offer a brief explanation on how you see it being integrated?

Thanks,
	Charlie

On Fri, 2004-10-08 at 19:44, Eric Pettersen wrote:
> 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
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
>