Arp/Warp

Morris RJ, Perrakis A, Lamzin VS. ARP/wARP s model-building algorithms. I. The main chain. Acta Cryst 2002 058 968-75. 

MR is an ensemble of techniques that aims to place and orientate an approximate molecular model in the unit cell of the crystal being studied. This will provide the starting phases needed to calculate the initial electron density map from which the protein model can be built, either manually by iterative use of reconstruction with molecular graphics packages (Jones et al., 1991) followed by refinement (Murshudov et al., 1997), or automatically if diffraction data up to 2.3 Angstroms or better are available (ARP/wARP (Perrakis et al., 2001), Solve/Resolve (Terwilliger, 2003)). 

Morris, R. J., Perrakis, A., and Lamzin, V. S. (2003). ARP/wARP and automatic interpretation of protein electron density maps. Method Enzymol. 374, 229-244. 

High resolution (between 1.4 and 2.0 A) Automated model building with ARP/wARP should work with most phase sets. RESOLVE, which uses a template-based rather than atom-based approach, should also perform well but may be computationally more consuming. Refinement can best be carried out with REEMAC or PHENIX using isotropic ADPs since the amount of data is no longer sufficient for an anisotropic description of atomic displacement parameters. The use of TLS (Winn et ah, 2003) is highly recommended. A use of NCS restraints should be critically evaluated and in most cases the refinement can proceed without them. Double conformations of side chains should be visible and modelled. Ordered solvent can be modelled automatically. 

Lamzin, V. S., Perrakis, A. and Wilson, K. S. (2001). The ARP/wARP suite for automated construction and refinement of protein models. In International Tables for Crystallography. Volume F Crystallography of biological macromolecules, Rossmann, M. G. and Arnold, E. eds., pp. 720-722. Dordrecht, Kluwer Academic Publishers, The Netherlands. 

The beta version of the warpNtrace procedure in ARP/wARP version 5 was then employed to improve the quality of the maps (53, 54). This procedure alternates between ARP, real space evaluation of atoms including the addition and removal of atoms and real space refinement, and reciprocal space refinement using the CCP4 program Refinac (55). After every tentii cycle, the resulting map is auto-traced, and the auto-traced structure is then subjected to additional cycles of the ARP / Refinac refinement. 

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