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 Results for DC.creator="R." AND DC.creator="W." AND DC.creator="Grosse-Kunstleve"   page 2 of 3 pages.
CNS, a program system for structure-determination and refinement
Brunger, A. T., Adams, P. D., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Pannu, N. S., Read, R. J., Rice, L. M. and Simonson, T.  International Tables for Crystallography (2012). Vol. F, ch. 18.6, pp. 512-519 [ doi:10.1107/97809553602060000860 ]
... facility is made for cross-validating statistical properties, such as R values (Brünger, 1992), values (Kleywegt & Brünger, 1996; Read ... structure factors. The `save' function computes the statistical average where w is 1 and 2 for centric and acentric reflections, respectively ... gratefully acknowledged. References Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Cross-validated ...

Symmetry in reciprocal space
Shmueli, U., Hall, S. R. and Grosse-Kunstleve, R. W.  International Tables for Crystallography (2010). Vol. B, ch. 1.4, pp. 114-174 [ doi:10.1107/97809553602060000761 ]
... cell, is the structure factor at the point h and r is a position vector of a point in direct space ... following two basic blocks:andwhere each of p, q and r can be a sine or a cosine, and appears at ... Seitz's product of two operators of affine transformation:where R is a matrix, is a row vector, r is ...

Model building
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 18.11.4.1, p. 541 [ doi:10.1107/97809553602060000865 ]
Model building 18.11.4.1. Model building Phenix.find_helices_strands will rapidly build a secondary-structure-only model into a map or very rapidly trace the polypeptide backbone of a model into a map. To build secondary structure in a map, phenix.find_helices_strands identifies [alpha]-helical regions and [beta]-strand segments, models ...
     [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 ]
... laws are present. If a model has been supplied, an R versus R (Lebedev et al., 2006) analysis is carried out. This type ... E., Black, K. D., Islas, L. D., Sankaran, B. & Zagotta, W. N. (2007). Structure and rearrangements in the carboxy- ...

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 ]
... with minimal modification, using the same underlying configuration system (libtbx.phil; Grosse-Kunstleve et al., 2005) as used by most PHENIX programs as ... al., 2005), the AutoSol (Terwilliger et al., 2009), AutoBuild (Terwilliger, Grosse-Kunstleve, Afonine, Moriarty, Adams et al., 2008) and LigandFit (Terwilliger et ... phenix.refine with a model pre-loaded. References Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). The Phenix ...
     [more results from section 18.11.1 in volume F]

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 ]
... presented in the context of crystallography, can be found in Grosse-Kunstleve et al. (2002). In addition to the advantages outlined ... combined use of Python and C++ can be found in Grosse-Kunstleve et al. (2002) and Abrahams & Grosse-Kunstleve (2003). This model is used throughout the PHENIX ...

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 ]
... the model using different random seeds for each iteration (Terwilliger, Grosse-Kunstleve et al., 2007). The variability in the coordinates of ... of the position of that atom. References Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). The Phenix refinement ...
     [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 ]
... for covalently bound ligands are also generated. References Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. (2009). electronic Ligand Builder ...
     [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]

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