[chimera-dev] ribbon for circular molecule

[Thomas Goddard]

Hi Volodymyr,

   Chimera is not easy to compile because it requires about 40 
third-party libraries as described on the Chimera source code page (link 
is on the Chimera download page).

	http://www.cgl.ucsf.edu/chimera/sourcecode.html

Also there is a bit of third-party surface calculation code which we are 
not allowed to distribute.  All the source code is viewable with the web 
interface to the SVN repository.  We also have a ticket active for 
allowing public access to check-out the entire Chimera SVN tree

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/7641

but that has not been done yet.

   If your purpose is to make a figure that doesn't have a gap in the 
circular molecule then the following trick might achieve that.  You 
could make a new molecule that is not closed and has the two starting 
residues duplicated at the end (with increasing residue numbers).  Then 
when you show the ribbon there will be an overlapping stretch.  Because 
the overlap will not be perfect you can hide the ribbon for one of each 
duplicated residue.  If you add a couple duplicate residues the ribbon 
should come into exact alignment with itself.

   I've added your request for circular ribbons to our feature request list.

	http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests

   If you can live with circular cross-section tube a command like

	shape tube :1-125.A at CA:1.A at CA radius 1

could do it but it does not close nicely -- different tangent vector and 
coloring and selection is not as flexible -- the tube is just a surface 
model.

	Tom


> Dear Sirs,
> 
> I am writing to ask for the chimera sources -- I would like to
> visualize a circular molecule using ribbons. As far as I can tell,
> with the current code ribbons always have ends (cannot be closed)
> because of the following snipped from
> 
> libs/_chimera/Chimera.toolkit/Ribbon.implementation
> 
> 696	Molecule::updateRibbonData()
> 697	{
> 698	        clearRibbonData();
> 699
> 700	        //
> 701	        // For each residue, find the residues before and after. 702	 
>       // Note that only residues with valid guide and plane atoms 703	    
>    // may be used as the prev/next residue in a ribbon.
> 704	        //
> 705	        std::map<Residue *, RibbonResidue> rrMap;
> 706	        Residue *prev = NULL;
>                 ^^^^^^^^^^^^^^^^^^^^^
> 
> Could you please allow me to check out the svn version of the
> chimera or get (easily compilable) sources of a recent release.
> 
> Thank you,
> 
> Volodymyr
> 
> 
> 
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