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RIBBON(1)		    General Commands Manual		     RIBBON(1)

       ribbon -	Raster3D molecular graphics package ribbon-drawer

	  "ribbon" [-h]	[-d[0123456]] pdbfile
	  "ribbon" [-h]	-d[0123456] -	  (to take PDB records from stdin)

       Ribbon reads a PDB coordinate file and produces a file on stdout	con-
       taining Raster3D	descriptor records for a ribbon	representation con-
       structed	from a triangular mesh.	 The file produced by ribbon may be
       fed directly to render or it may	be combined with descriptor files pro-
       duced by	other Raster3D utilities.

       To describe a the entire	protein	chain as a single ribbon colored
       smoothly	from blue at the N-terminus to red at the C-terminus:

	    ribbon -d2 protein.pdb | render > chain_picture.png

       To color	a multi-chain protein with specified colors for	each chain:

	    cat	chaincolors.pdb	protein.pdb | ribbon -d5 - > chains.r3d


       Suppress	header records in output.  By default ribbon will produce an
       output file which starts	with header records containing a default set
       of scaling and processing options.  The -h flag will suppress these
       header records so that the output file contains only triangle descrip-
       tors.  This option is useful for	producing files	which describe only
       part of a scene,	and which are to be later combined with	descriptor
       files produced by other programs.


       By default ribbon requires interactive input to select ribbon parame-
       ters and	coloring information.  Five default coloring schemes are im-
       plemented, however, and these may be selected as	a command line option
       to bypass any interactive input.

	-d or -d0     same as -d2 below

	-d1 solid color	ribbon (defaults to blue)

	-d2 shade from blue at N-terminus to red at C-terminus

	-d3 one	surface	of ribbon is blue, other surface is grey

	-d4 shade front	surface	from blue to red, back surface is grey

	-d5 color separate chains using	successive color cards
	    from input stream. Note that pattern matching on the color records
	    is _not_ done; colors are simply taken sequentially	as new chains
	    are	encountered.

	-d6 Color by nearest CA	atom as	taken from the COLOUR
	    records at the head	of the input file

       The input to ribbon consists of a single	text file containing colour
       information [optional] and atomic coordinates in	PDB data bank format.
       Only CA and carbonyl O atom records are required; all other input atoms
       are ignored.  Ribbon parameters and colouring specified interactively
       when the	program	is run.	 Keyboard interaction may be bypassed by se-
       lecting one of the default colouring schemes using the -d flag.	A tri-
       angular mesh ribbon is output as	Raster3D descriptor records.  By de-
       fault the output	file contains a	set of header records as required by
       the render program.  The	header is constructed to include a TMAT	matrix
       corresponding to	the transformation matrix contained in file
       trix (if	it exists), or to the Eulerian angles contained	in file
       setup.angles (if	it exists).

       Ribbon produces a continuous smooth trace of the	protein	backbone.  For
       more complicated	representations	of protein secondary structure it is
       better to use a different program, e.g. MOLSCRIPT, rather than ribbon.

       The files setup.matrix and setup.angles,	if they	exist, affect the
       header records produced by ribbon.

       anonymous ftp site:

       web URL:

	    Ethan A Merritt
	    University of Washington, Seattle WA 98195

       MOLSCRIPT(l), render(l),	rods(l), balls(l)

       Original	ribbon code written by Phil Evans for the CCP4 version of
       FRODO.  Modification to describe	solid ribbons as triangular mesh for
       Phong shading in	Raster3D package by Ethan A Merritt.

Raster3D			  8 May	1999			     RIBBON(1)


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