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normal3d(1) [debian man page]

NORMAL3D(1)						      General Commands Manual						       NORMAL3D(1)

NAME

       normal3d - apply transformation matrix in Raster3D input file

SYNOPSIS

       normal3d [options] < infile.r3d > normalized.r3d

DESCRIPTION

       normal3d reads a Raster3D input file from stdin, applies any coordinate manipulations specified in the header, and writes the modified file
       to stdout.

       The output file from normal3d describes exactly the same image as the original input file. Header records are left unchanged except for the
       transfomation matrix (which becomes the identity matrix) and the format specifiers (which are set to *). The -h flag suppresses all header
       records in the output file.  All objects in the input file are also in the output file, but their coordinate descriptions have been normal-
       ized (i.e. the original transformation matrix has been applied).

OPTIONS

       -ang AA

       Only relevant for generating stereo pairs. By default stereo separation is created using a shear operator. The -ang option instead intro-
       duces an angular separation by rotating the left and right eye images by +/- AA degrees with respect to the original view angle.

       -expand

       In-line and normalize all instances of file indirection in the input stream.  This results in a single input file containing no file indi-
       rection.  The default is to simply copy file indirection lines (those begining with @) to the new input file without opening them or nor-
       malizing their contents.

       -h

       Suppress header records in output.  This option is useful for producing files which describe only part of a scene, and which are to be
       later combined with descriptor files

       -size HHHxVVV

       Force the image size to HHH pixels horizontal and VVV pixels vertical.

       -stereo [scratch]

       This option causes the program to produce two additional files, left.r3d and right.r3d, that contain header records suitable for rendering
       the normalized object desctiption file as a side-by-side stereo pair.  This option always suppresses header records in the primary output
       file.  If a scratch directory name is given, it is prepended to give output files {scratch}_left.r3d and {scratch}_right.r3d

SOURCE

       web URL:
	    http://www.bmsc.washington.edu/raster3d/raster3d.html

       contact:
	    Ethan A Merritt
	    University of Washington, Seattle WA 98195
	    merritt@u.washington.edu

SEE ALSO

       render(l), raster3d(l), stereo3d(l)

AUTHORS

	Ethan A Merritt.

Raster3D							    12 Dec 2010 						       NORMAL3D(1)

Check Out this Related Man Page

RINGS3D(1)						      General Commands Manual							RINGS3D(1)

NAME

       rigns3d - produces a file of ring-filling triangles from a PDB file

SYNOPSIS

       rings3d [-bases] [-protein] [-sugars]  < infile.pdb > outfile.r3d

       rings3d searches through a PDB file looking for residues containing 5- or 6-membered rings, then produces a Raster3D output file of ring-
       filling triangles.

       rings3d matches residue types from an internal list of residue and atom names. It will fail to find residues not in its list, and fail to
       recognize atoms with non-standard names.

EXAMPLES

       render a DNA molecule with the bases filled in:

	    cat $R3D_LIB/dna.colours dna.pdb | rods -radius 0.05 > temp.1
	    rings3d -bases < dna.pdb > temp.2
	    cat temp.1 temp.2 | render -tiff dna.tiff

OPTIONS

       -bases

       Fills in purine and pyrimidine rings from A C G T U residues.

       -protein

       Fills in sidechain rings of HIS PHE TRP and TYR residues.

       -sugars

       [This is the default] Fills in pyranose rings of GAL GLC NAG NGA MAN SIA residues.

BUGS

       limited residue types

       The database of residue types should be kept externally, so you don't have to rebuild the program to add a new type.  There should be an
       option to search for ring systems in un-recognized residue types.  crinkled planes

       There should be an option to do a least-squares best plane through supposedly flat rings. Then again, seeing a crease in a "flat" ring may
       force people to consider whether their planarity restraints are tight enough.

SOURCE

       anonymous ftp site:
	    ftp.bmsc.washington.edu

       web URL:
	    http://www.bmsc.washington.edu/raster3d/raster3d.html

       contact:
	    Ethan A Merritt
	    Dept of Biological Structure Box 357742
	    University of Washington, Seattle WA 98195
	    merritt@u.washington.edu

SEE ALSO

       Raster3D(l)

AUTHORS

       Ethan A Merritt.

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others).

Raster3D																RINGS3D(1)
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