This analysis began with the PDB entry 6LU7. The structure has been prepared as follows.

Downloaded from PDB repository.
Note that this structure contains the protease structure as chain A and an inhibitor as chain C.
Opened in PyMOL v0.99.
Symmetry applied; symmetry mate selected to form homodimeric structure; symmetry mate chain reset to B; symmetry mate of inhibitor chain reset to D; homodimer saved including inhibitors.
Homodimer processed using the MolProbity website to add hydrogens at electron-cloud positions, including flipping of ambiguous residues where suggested.
Hydrogenated homodimer opened in PyMOL v0.99; heteroatoms, mostly water residues, removed, but inhibitor retained; alternative side chain configurations removed; structure saved as "6lu7inhib.pdb".`

Covalent, hydrogen-bond and hydrophobic interactions identified based on structure geometry and saved in files cov.in, hbonds.in, hphobes.in. hphobes.in has been edited to remove a phobic tether linking ALA285 of each chain and tethers linking LEU286 of one chain to THR280 of the other, as examination of the structure suggested that these tethers were not appropriate as a permanent constraint in the system. This bond analysis was carried out using the SBFIRST utility, a copy of which is included with this data set. The .in files are suitable for use as input to the rigidity analysis software FIRST, from Arizona State University. The stacked.in file is empty (would hold stacked-ring interactions in nucleic acid structures).

Static rigidity analysis of the structure is carried out in the folder Clusters. Normal mode analysis identifying nontrivial low-frequency modes intrinsic to the structure is carried out in the folder Modes. Geometric simulations of flexible motion along the normal mode directions is carried out in the folder Runs, controlled by the bash script file loopFRODA.sh.