[Chimera-users] new snapshot release (1.1917)

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 9 16:02:09 PST 2004

	We've just put a new snapshot release of Chimera up for download on 
the web site (http://www.cgl.ucsf.edu/chimera).  Here are the 
highlights of the changes between this snapshot (1.1917) and the 
previous one (1.1892):

		Match -> Align can create sequence alignments for multiple matched 
			(not just pairs)
		Multalign Viewer can show/edit sequence annotations for relevant 
			(RSF, Stockholm)
			-- saves label font/size and secondary structure assignments
			-- compiles to .pyc file:  50% less memory use, 15% less time to 
		added Export Surfaces as VRML (in Utilities category)
			-- save surfaces made by Multiscale Models and Volume Viewer as VRML 
		added Browser Configuration (also in Utilities)
			-- configure browsers to send certain file types to Chimera
			(see also new Web Data preferences)
		FindHBond and PBReader allow line width to be set
		Movie has preliminary support for reading GROMOS trajectories
	newly available commands:
		bondcolor -- color bonds independent of flanking atoms
		bonddisplay -- set how bond display depends on flanking atom display
		bondrepr -- set bond representation to be wire or stick (independent 
of atoms)
		hbonds -- command equivalent of FindHBond tool
		rlabel -- whether residue name/number is included in the first atom 
label per residue
	Model Panel
		new 'render attrs...' button allows coloring by model/residue/atom 
			(e.g. B-factor)

The 'render attrs...' interface is in preliminary form and will be 
changing.  It also isn't documented yet but is pretty easy to use.  
Just pick an attribute of interest and a histogram of values will be 
displayed.  By default there will be three color bars on the histogram 
that you can grab and move around with the mouse, or add or remove with 
control-click.  You can use the 'Color' color well to set the color of 
the last bar you picked.  The 'No value' color well is used in the rare 
case of the attribute being missing (or set to None) in the 
atom/residue/model.  Click Apply or OK to make the coloring happen.  
Several parts of the interface are grayed out since they haven't been 
implemented yet.  In the future you will be able to select by attribute 
value, and change atom radii or ribbon widths based on attribute values.

If you are using the last production release (1.1872) instead of the 
previous snapshot, then you will also be getting these features when 
you go to 1.1917:

		additional file formats for saved images (PS, EPS)
		different lighting scheme in graphics window (over-the-shoulder 
instead of headlight)

		added Shininess Control (in Viewing Parameters)
			-- adjust shininess, brightness, and the color used for shiny 
		Collaboratory section in Preferences allows designation of port 
number and IP address
			(for firewalls/NAT)
			-- allows definition of scripts to be run at each time step
			-- looping can be turned off

		Multalign Viewer allows structure selection by arbitrary % residue 

		Volume Viewer options added to subdivide and smooth isosurfaces

		copy command now offers supersampling and PS/EPS formats
		new ribbackbone command controls whether ribbon and backbone atoms 
are shown simultaneously


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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