6.4.8. PROTEIN DATA BANK (PDB) FORMAT

next, previous Section / Table of Contents / Index This format can be used to save structure information from LATTICE and CLUSTER sessions using the Brookhaven Protein Data Bank (PDB) format. All (visible) atoms of a lattice section or cluster are icluded by their element names and cartesian coordinates only while section size, periodicity, or graphics definitions are lost. PDB format (last draft version 2.1, October 25, 1996, (C) Brookhaven National Laboratory) files can serve as input to many different molecular visualization and database packages, such as Rasmol, WebLab Viewer by Molecular Simulations Inc., and others. BALSAC uses only a restricted PDB format described in the following. In particular, crystal periodicity of a BALSAC/LATTICE session will not be saved in PDB format. For further details consult the Protein Data Bank Contents Guide published by Biology Dept., Bldg. 463, Brookhaven National Laboratory, P. O. Box 5000, Upton, NY 11973-5000 (USA). Of the complete PDB type structure file format only the following 4 Cards are included: Card 1. ('TITLE ',A72) TTT TTT := Title text of the lattice section / cluster. Card 2. ('AUTHOR BALSAC by K. Hermann (C) Fritz-Haber-Institut ', 'Berlin 1999') BALSAC identification and copyright. Card(s) 3. ('ATOM',I7,1X,A2,16X,3F8.3) (I,NAME(I),X(I),Y(I),Z(I),I=1,NKTOT) I := Number of the Ith atom in the lattice section or cluster. NAME := Element symbol of the Ith atom in the lattice section or cluster. X(I),Y(I),Z(I) := Cartesian coordinates of the Ith atom. Card 4. ('END') := Last Card of file. The following listing shows as an example the output file of an interactive BALSAC/CLUSTER session with input from the PLOT3D format example file given in Sec. 6.4.3. The sequence of lines refers to Cards no. 1, 2, 3, 4. ----------------------------------------------------------------------------- TITLE Ni(CO)4 real coordinates AUTHOR BALSAC by K. Hermann (C) Fritz-Haber-Institut Berlin 1999 ATOM 1 Ni .000 .000 .000 ATOM 2 C -1.580 1.580 1.580 ATOM 3 O -3.220 3.220 3.220 ATOM 4 C 1.580 -1.580 1.580 ATOM 5 O 3.220 -3.220 3.220 ATOM 6 O 3.220 3.220 -3.220 ATOM 7 C 1.580 1.580 -1.580 ATOM 8 C -1.580 -1.580 -1.580 ATOM 9 O -3.220 -3.220 -3.220 END ----------------------------------------------------------------------------- next, previous Section / Table of Contents / Index