You can change parameters of program by modifying the System/TOPOS Parameters submenu.
The Default Radii System option determines the system of radii that is used by the IsoCryst and AutoCN programs. The colour of atoms can be changed by the Change Colours button. Select the atom and modify its colours as you want. The button Change Font allows to change the font of legend of atoms in IsoCryst program. The Min. Valid Dist. value is used as a criterion for too short interatomic distances in such procedures as Compound/Auto Determine/Errors in Distances or Remove Doubled Atoms. The ToposPro applied programs use this criterion at the initial stage to estimate if the structure is valid or not. Usually, you should not change this criterion. The Multiplier for Radii criterion (MR) is used to find “chemically” short interatomic distances: the distance R(A-B) is short if R<(rA+rB)⋅MR, where rA and rB are taken from Default Radii System. The Extra Dist. criterion (ED) is used in the AutoCN Domains and Ranges algorithms when comparing the distance R(A-B) with (rA+rB)(1+ED) to solve if the distance corresponds to chemical bond. Bond Valence Parameters determines the data for calculation of bond valences; the parameters can be taken from the paper by Brese, N. E., O'Keeffe, M. Bond-valence parameters for solids. Acta Cryst. 1991, B47, 192-197 or from an external BVPARM.CIF file, which should be placed into the ToposPro folder.
If you want to extract the information about cell parameters and bibliography, you can select the corresponding flags in Output tab. Also the format of the output information can be chosen.
Then just select compounds and press F9 key. The window with requested information will appear.
Systre format is the input file for Systre (http://www.gavrog.org), and it is useful if you need to check new nets. CIF exports the crystallographic data to the .cif format readable with many free programs (e.g. Mercury), BUT remember that the adjacency matrix is not exported.
If you want a reproduction of exactly what you see on Isocryst window, you can export the selected view as .pdb file, readble by Mercury, Jmol, RasMol.
The tab Paths contains location addresses of program ToposPro/TTD collection/TTO collection/graph-files.