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RODS(1)			    General Commands Manual		       RODS(1)

       rods - Raster3D preprocessor for	ball-and-stick models

       Rods reads a file describing atom colours and/or	a PDB coordinate file
       and produces a file containing Raster3D descriptor records.  The	file
       produced	by rods	may be fed directly to render or it may	be combined
       with descriptor files produced by other Raster3D	utilities.

       To describe a simple bonds-only model coloured by residue type:

	    cat	mycolours.pdb protein.pdb | rods | render > mypicture.png

       To render the same molecule as ball-and-stick:

	    cat	mycolours.pdb protein.pdb | rods -b | render > mypicture.png


       Suppress	header records in output.  By default rods 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 object 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 rods will describe bonds only; the -b	flag will cause	it to
       include spheres at the atom positions also, yielding a ball-and-stick

       -radius R

       By default rods will draw bonds as cylinders with a 0.2A	radius.	 The
       radius option allows you	to change this cylindrical radius.

       -Bcolor Bmin Bmax

       Assign colors based on B	values rather than from	atom or	residue	types.
       Atoms with B <= Bmin will be colored dark blue; atoms with B >= Bmax
       will be colored light red; atoms	with Bmin < B <	Bmax will be assigned
       colors shading smoothly through the spectrum from blue to red.

       The input to rods consists of a single text file	containing colour in-
       formation and atomic coordinates	in PDB data bank format.  Coordinates
       are output as Raster3D descriptor records with colours and sphere radii
       assigned	according to the COLO records described	below.	Ball-and-stick
       figures have atoms drawn	at 0.2 * VanderWaals radius, connected by rods
       with a default 0.2A cylindrical radius.	Bonds are drawn	for atoms
       which lie closer	to each	other than 0.6 * (sum of VanderWaals radii).
       By default the output file contains a set of header records as required
       by the render program.  The header is constructed to include a TMAT ma-
       trix corresponding to the transformation	matrix contained in file
       setup.matrix (if	it exists), or to the Eulerian angles contained	in
       file setup.angles (if it	exists).

       Colours are assigned to atoms using a matching process, using COLOUR
       records prepended to the	input PDB file.	 If no COLOUR records are
       present in the input file, atoms	will  receive default CPK colors
       (C=grey,	O=red, N=blue, S=yellow, P=green, other=magenta).  Raster3D
       uses a pseudo-PDB record	type with the same basic layout	as the above
       but with	COLO in	the first 4 columns:


	   1 -	4   COLO

	   7 - 30   Mask (described below)

	  31 - 38   Red	component

	  39 - 46   Green component

	  47 - 54   Blue component

	  55 - 60   van	der Waals radius in Angstroms

	  61 - 80   Comments

       Note that the Red, Green, and Blue components are in the	same positions
       as the X, Y, and	Z components of	an ATOM	or HETA	record,	and the	van
       der Waals radius	goes in	place of the Occupancy.	 The Red, Green, and
       Blue components must all	be in the range	0 to 1.

       The Mask	field is used in the matching process as follows.  First the
       program reads in	and stores all the ATOM, HETA, and COLO	records	in in-
       put order.  Then	it goes	through	each stored ATOM/HETA record in	turn,
       and searches for	a COLO record that matches the ATOM/HETA record	in all
       of columns 7 through 30.	 The first such	COLO record to be found	deter-
       mines the colour	and radius of the atom.

       In order	that one COLO record can provide colour	and radius specifica-
       tions for more than one atom (e.g., based on residue or atom type, or
       any other criterion for which labels can	be given somewhere in columns
       7 through 30), the "#" symbol is	used as	a wildcard. I.e. a # in	a COLO
       record matches any character in the corresponding column	in an ATOM or
       HETA record.  All other characters must match literally to count	as a
       match.  Note that the very last COLO record in the input	should have #
       symbols in all of columns 7 through 30 in order to provide a colour for
       any atom	whose ATOM/HETA	record fails to	match any previous COLO
       record.	This idea of matching masks for	colour specifications is due
       to Colin	Broughton.

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

       web URL:

	    Ethan A Merritt
	    University of Washington, Seattle WA 98195

       render(l), ribbon(l), balls(l)

	    Ethan A Merritt

Raster3D			   8 May 1999			       RODS(1)


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