Skip to main content
. Author manuscript; available in PMC: 2012 Jun 1.
Published in final edited form as: Methods. 2010 Dec 14;54(2):239–250. doi: 10.1016/j.ymeth.2010.12.010

Fig. 8.

Fig. 8

A near-closed tectosquare found in an automated search for such combinations of the building blocks (KL and L-shaped monomers) performed with the aid of PyMOL scripts. Four sets of mutated KL-complexes (green, blue, red, magenta) to be used in the best closure search were selected in preliminary runs (refer to Sections 4.1 and 4.3 for details). These sets of solutions with gaps within 6 Å were then used as input to search for best closures including the dynamic states of L-shaped monomers. In the final phase the best scoring KL and L-shape MD states were used in a search for the best closure combinations. Note that the improvement in the gap score over the parameter-guided search illustrated in Fig. 7 came from a selection of more distorted MD states with lower torsion angles (listed under every KL label). The RMSD values of each fit in the chain assembly are listed next to each side of every KL. The overall improvement in the quality of closure fit over the structure shown in Fig. 7 is best captured in the C2D1 edge view, in which the final gap is seen on the left side of the C2D1 KL complex.