ClusterGeom is a Java program that uses circumspheres and circumcircles to assess distorsion in iron-sulfur clusters. ClusterGeom4, which is the module that analyzes [4Fe-4S] clusters, was described in:
Fee, J.A.; Castagnetto, J.M.; Case, D.A.; Noodleman, L., Stout, C.D.; Torres, R.A. "The cirscumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526. (On-line copy of the paper).(See also the supplementary material for this paper).
The geometrical analysis begins with a structure file (in PDB format) that describes the positions of the Fe, S, and SG atoms in 3-space or a *.cif file that also contains error information, and calculates the circumcenter (CC) positions and radii of the three circumspheres. The program moves CCFe to 0,0,0 (the origin) by translating all atom and circumcenter positions along parallels to the CCFe to (0,0,0) vector. The Fe1 to CCFe vector is typically used to define the x-direction and either Fe2, Fe3, or Fe4 can be chosen to lie in the xy-plane thereby fixing the cluster in a Cartesian coordinate system having CCFe at its center. The program calculates the spherical coordinates of each atom on its respective Fe, S and SG circumsphere. Three radii, three circumcenter positions, and twelve geospherical atom positions {longitude (θ), latitude (φ)} define the structure of the cluster.
Output includes circumcenter positions, radii, geospherical coordinates of the individual atoms {θ, φ}, and Hammer-Aitoff projections (xy) on a unitary sphere to which 35.25º are added to all longitudes in order to center the cluster on the projection. Standard deviations of these parameters are calculated using expressions for error propagation and knowledge of unit cell dimensions and angles obtained from the final least squares (L.S.) structure refinement by the SHELX program. The maximum error in the circumcenter positions (CCFe, CCS, and CCSG) are obtained for each atom position denoted by the 3x3 matrix {xi, yi, zi; xi ± δxi; yi ± δyi; zi ± δzi} followed by calculating the average position about {xi, yi, zi} for each four atom set.
The ClusterGeom4 Java application, along with a representative I/O files and a Unix/Linux shell script can be downloaded as a ZIP file.