Model morphing and sequence assignment after molecular replacement.

A procedure termed `morphing' for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package

A deformed analogue of Onsager's symmetry in the XXZ open spin chain

The XXZ open spin chain with general integrable boundary conditions is shown to possess a q-deformed analogue of the Onsager's algebra as fundamental non-abelian symmetry which ensures the integrability of the model. This symmetry implies the existence of a finite set of independent mutually commuting nonlocal operators which form an abelian subalgebra. The transfer matrix and local conserved quantities, for instance the Hamiltonian, are expressed in terms of these nonlocal operators. It follows that Onsager's original approach of the planar Ising model can be extended to the XXZ open spin chain.Comment: 12 pages; LaTeX file with amssymb; v2: typos corrected, clarifications in the text; v3: minor changes in references, version to appear in JSTA

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.

An approach is presented for addressing the challenge of model rebuilding after molecular replacement in cases where the placed template is very different from the structure to be determined. The approach takes advantage of the observation that a template and target structure may have local structures that can be superimposed much more closely than can their complete structures. A density-guided procedure for deformation of a properly placed template is introduced. A shift in the coordinates of each residue in the structure is calculated based on optimizing the match of model density within a 6 Å radius of the center of that residue with a prime-and-switch electron-density map. The shifts are smoothed and applied to the atoms in each residue, leading to local deformation of the template that improves the match of map and model. The model is then refined to improve the geometry and the fit of model to the structure-factor data. A new map is then calculated and the process is repeated until convergence. The procedure can extend the routine applicability of automated molecular replacement, model building and refinement to search models with over 2 Å r.m.s.d. representing 65-100% of the structure

The Erd\H{o}s-Ko-Rado theorem for twisted Grassmann graphs

We present a "modern" approach to the Erd\H{o}s-Ko-Rado theorem for Q-polynomial distance-regular graphs and apply it to the twisted Grassmann graphs discovered in 2005 by van Dam and Koolen.Comment: 5 page