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PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, ch. 18.11, pp. 539-547 [ doi:10.1107/97809553602060000865 ]
... AutoSol (Terwilliger et al., 2009), AutoBuild (Terwilliger, Grosse-Kunstleve, Afonine, Moriarty, Adams et al., 2008) and LigandFit (Terwilliger et al., 2006 ... E2 - 1|> values, the L statistic (Padilla & Yeates, 2003) and N(Z) plots are derived from data cut to theresolution limit ... from all calculations of structure factors (Terwilliger, Grosse-Kunstleve, Afonine, Moriarty, Adams et al., 2008). The phenix.autobuild iterative-build ...

Iterative model building, density modification and refinement
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.7.3, pp. 544-545 [ doi:10.1107/97809553602060000865 ]
... of that atom. References Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). The Phenix refinement framework. CCP4 ... Cryst. D60, 2144-2149. Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Adams, P. D., Moriarty, N. W., Zwart, P., Read, R. J., Turk, D. & ...
     [more results from section 18.11.7 in volume F]

Ligand-coordinate and restraint-geometry generation
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.6.1, pp. 543-544 [ doi:10.1107/97809553602060000865 ]
... geometry generation The electronic Ligand Builder and Optimization Builder (eLBOW; Moriarty et al., 2009) is a suite of tools designed for ... files required for covalently bound ligands are also generated. References Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. (2009) ...
     [more results from section 18.11.6 in volume F]

Model and structure-factor manipulation and analysis
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.5.1, pp. 542-543 [ doi:10.1107/97809553602060000865 ]
Model and structure-factor manipulation and analysis 18.11.5.1. Model and structure-factor manipulation and analysis PHENIX has a range of tools for displaying, analysing and manipulating structure-factor and model information. Phenix.mtz.dump and phenix.cif_as_mtz display and convert structure-factor data. Phenix.print_sequence, phenix.pdb_atom_selection and phenix.pdbtools display and ...
     [more results from section 18.11.5 in volume F]

Maps, models and avoiding bias
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.4.4, p. 542 [ doi:10.1107/97809553602060000865 ]
... from all calculations of structure factors (Terwilliger, Grosse-Kunstleve, Afonine, Moriarty, Adams et al., 2008). The phenix.autobuild iterative-build OMIT ... from atomic models. Acta Cryst. A51, 880-887. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Refinement of ... Cryst. A42, 140-149. Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., ...
     [more results from section 18.11.4 in volume F]

Noncrystallographic symmetry (NCS)
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.3.3, pp. 540-541 [ doi:10.1107/97809553602060000865 ]
Noncrystallographic symmetry (NCS) 18.11.3.3. Noncrystallographic symmetry (NCS) Noncrystallographic symmetry is an important feature of many macromolecular crystals that can be used to greatly improve electron-density maps. PHENIX has tools for the identification of NCS and for using NCS and multiple crystal forms of a macromolecule in phase improvement. Phenix.find_ncs ...
     [more results from section 18.11.3 in volume F]

Analysis of experimental data
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.2, p. 540 [ doi:10.1107/97809553602060000865 ]
... E2 - 1|> values, the L statistic (Padilla & Yeates, 2003) and N(Z) plots are derived from data cut to theresolution limit ... E., Black, K. D., Islas, L. D., Sankaran, B. & Zagotta, W. N. (2007). Structure and rearrangements in the carboxy-terminal ...

Graphical user interface
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.1.2, p. 539 [ doi:10.1107/97809553602060000865 ]
... AutoSol (Terwilliger et al., 2009), AutoBuild (Terwilliger, Grosse-Kunstleve, Afonine, Moriarty, Adams et al., 2008) and LigandFit (Terwilliger et al., 2006 ... model pre-loaded. References Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). The Phenix refinement framework. CCP4 Newsl. 42, contribution 8. DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano ...
     [more results from section 18.11.1 in volume F]

Conclusions
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H.  International Tables for Crystallography (2012). Vol. F, Section 18.11.8, p. 545 [ doi:10.1107/97809553602060000865 ]
Conclusions 18.11.8. Conclusions Advances in computational methods and algorithms have made it possible to automate the solution of many structures with PHENIX. However, many challenges still exist. In particular, the development of automated methods that can be applied at low resolution (worse than 3.0Ć) remains a priority. In this resolution range ...

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