3D-lattice protein

Jon Leech leech at cs.unc.edu
Tue Mar 15 13:44:51 EST 1994

In article <2lne9v$otq at hermod.uio.no>, rushing at titan.ksc.nasa.gov (Sam Rushing) writes:
|> In article <Pine.3.85.9403081855.A15756-0100000 at fox.cce.usp.br>, szeinfel at FOX.CCE.USP.BR (Rafael N Szeinfeld) says:
|> >	    I would like to know if there is any program that takes as input
|> >a pdb file with atomic coordinates of a protein (let's say from Brokheaven
|> >protein databank) and inserts it in a cubic lattice (you define the
|> >dimensions of the unit cell) so that as output you have a matrix M(AxBxC)
|> >where each element of the matrix M(i,j,k)=1 if the this unit cell is
|> >ocuppied by one or more atoms or M(i,j,k)=0 if this unit cell is empty.
|> >
|> very good idea and it's new, so I think you won't have chance to find out an
|> existing program.

    This is analogous to a voxel representation of the protein, so you might
look into computer graphics volume rendering codes. Some of them have
modules to convert geometry to voxels, which is the same idea.

    Are you defining occupancy solely by the geometric position of atoms, or
assuming an atom occupies some volume as well?


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