This module extracts the backbone elements from a PDB file. The elements are
then connected and the chain ends determined. The elements are then sorted
by sequence in the chain. NOTE: element id's are assigned so that the N's
have id's of 0,4,8... the alpha carbons, 1,5,9... and so on. The
output is a Chemistry Pyramid. The connectivity is determined by the
standard vdw test.
Filename -- File Browser
Filename of PDB file
Molecule -- Pyramid
(n-layer, optional-baseLat, n-D compression, n-compression type).
The output is a Chemical-based pyramid. This pyramid has 2
layers of lattices. The base layer (0) contains the bond order
and 2 atom numbers that comprise the bond. The next layer (1),
contains the connectivity information, atom data, and the cartesian
coordinates. Eact atom has 4 data variables: ID, element number
vdw radius, and colour number.
NOTE: Here element id's do not correspond to id's in the PDB file.