AVS Modules						     pdb to geom(6)

NAME
     pdb to geom - create molecule geometry from Protein Data Bank(PDB)
     file

SUMMARY
     Name	   pdb to geom

     Type	   data

     Inputs	   none

     Outputs	   geometry

     Parameters	   _N_a_m_e		   _T_y_p_e		  _C_h_o_i_c_e_s
		   Data	file	   browser
		   Render Mode	   choice	  ball and stick, ball,	stick,
						  colored stick, colored residue

DESCRIPTION
     The pdb to	geom module reads the description of a molecule	from a file
     in	the Brookhaven Protein Data Bank (PDB) data format. Typically, such
     files have	a ._p_d_b filename	suffix.	The output is an AVS _g_e_o_m_e_t_r_y
     description of the	molecule.

PARAMETERS

     Data File
	  A file browser allows	you to specify the name	of the ._p_d_b file

	  containing the molecule description.

     Mode
	  The type of geometry produced:

	  ball and stick
	    Small spheres represent the	atoms, and white lines represent

	    the	bonds.

	  ball

	    Large spheres represent the	atoms.

	  stick

	    White lines	represent the bonds.

	  colored stick

	    Colored lines represent the	atoms and their	bonds.

	  colored residue
	    Colored lines represent the	atoms and their	bonds.	The color
	    of the lines represents the	type of	amino acid that	the
	    molecule is	in.

OUTPUTS

     Molecule (geometry)
	  An AVS _g_e_o_m_e_t_r_y description of the molecule.

EXAMPLE
     This example shows	a simple application of	pdb to geom:

				     PDB TO GEOM
					  |
				   GEOMETRY VIEWER

RELATED	MODULES
     geometry viewer, render geometry

LIMITATIONS
     If	you read in the	same ._p_d_b file name twice, you will get	only one
     instance of the geometry, not two.

     Since the ._p_d_b file does not contain any bond information,	bonding	is
     determined	by the distances between atoms.

SEE ALSO
     The example script	PDB TO GEOM demonstrates the pdb to geom module.

Release	4			    AVS			     pdb to geom(6)