Networks / Pajek
Package for Large Network Analysis

PDB Files


There are many PDB (Brookhaven Protein Databank format) files at: The PDB files can be directly viewed by (a helper application) Rasmol or by a plug-in Chime.

To get the last version of Mage for Windows look at Duke-BioChem FTP and for other information about Mage to Mage Home Page.

To use PDB files with Pajek you should transform them into MAC (preserves also colors) or BS (Ball and Stick) format. This can be done using program Babel ( ZIP for DOS). To transform graph.pdb into graph.mac or graph.bs request

babel -ipdb graph.pdb -omacmol graph.mac
babel -ipdb graph.pdb -obs graph.bs
There exists also an interface for Windows ( ZIP) - you will need also Babel for DOS.

After you read the BS file in Pajek you can try to draw it Draw/ Draw. To see it you should select Options/ Transform/ Fit Area and to control it activate scrollbars with Options/ ScrollBar On/Off.


PDB Files

File name #vert #arcs #edgs values time lines source
H2O.bs 3 0 2 00:00 4 BS; PDB
Butane.bs 14 0 13 00:00 15 BS; PDB
C6H12.bs 18 0 24 00:00 19 BS; PDB
Ethanol.bs 9 0 8 00:00 10 BS; PDB
Hexane.bs 20 0 19 00:00 21 BS; PDB
pdb101d.bs 556 0 579 00:00 557 BS; PDB
pdb201d.bs 0 00:00 BS; PDB
pdb201l.bs 2763 0 2686 00:00 2764 BS; PDB
pdb301d.bs 878 0 960 00:00 879 BS; PDB
1atn.bs 5020 0 5128 00:00 5021 BS; PDB
1crn.bs 327 0 337 00:00 328 BS; PDB
3cro.bs 1881 0 1966 00:00 1882 BS; PDB
Arb003.bs 221 0 226 00:00 222 BS; PDB

Pajek; Vlado/Networks