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ARP/wARP - automated model building and refinement
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, ch. 18.8, pp. 525-528 [ doi:10.1107/97809553602060000862 ]
... demanding and highly subjective step, heavily dependent on the researcher's experience, has been largely substituted by automated procedures. Automated model ... to proceed. ARP/wARP has built on two innovative concepts (Lamzin & Wilson, 1993, 1997; Perrakis et al., 1999). (1) It ... set of free atoms (Agarwal & Isaacs, 1977), as described by Lamzin & Wilson (1997), that have undefined chemical identity: these atoms ...

Iterations
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.4, p. 528 [ doi:10.1107/97809553602060000862 ]
Iterations 18.8.4. Iterations Building protein chains or solvent with ARP/wARP proceeds in an iterative fashion. When the quality of the (partially built) model is sufficiently high, the phases improve overall and result in an enhanced electron density where a more accurate and more complete model may be built. An important ...

Solvent building
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3.5, pp. 527-528 [ doi:10.1107/97809553602060000862 ]
Solvent building 18.8.3.5. Solvent building In this application, the protein model (together with bound metals, ligands or nucleic acids) is not rebuilt during refinement. Instead, only the solvent structure is continuously updated. Since ordered solvent in a typical crystal structure comprises about 10% of the model, improvement of solvent indirectly improves ...
     [more results from section 18.8.3 in volume F]

Free-atom and hybrid models
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.2, pp. 525-526 [ doi:10.1107/97809553602060000862 ]
... set of free atoms (Agarwal & Isaacs, 1977), as described by Lamzin & Wilson (1997), that have undefined chemical identity: these atoms are ... resolution map. Proc. Natl Acad. Sci. USA, 74, 2835-2839. Lamzin, V. S. & Wilson, K. S. (1997). Automated refinement for ...

Refinement and model building are two parts of modelling a structure
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.1, p. 525 [ doi:10.1107/97809553602060000862 ]
... to proceed. ARP/wARP has built on two innovative concepts (Lamzin & Wilson, 1993, 1997; Perrakis et al., 1999). (1) It ... resolution) and the quality of the initial phase estimates. References Lamzin, V. S. & Wilson, K. S. (1993). Automated refinement of ...

Applicability and requirements
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.5, p. 528 [ doi:10.1107/97809553602060000862 ]
... the future. References Skubák, P., Murshudov, G. & Pannu, N. S. (2009). A multivariate likelihood SIRAS function for phasing and ...

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