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 Results for articles by Chen, L.   page 1 of 2 pages.
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 ]
... merohedral cases. Amplitude and intensity ratios, <|E2 - 1|> values, the L statistic (Padilla & Yeates, 2003) and N(Z) plots are derived ... graphics visualized in three dimensions in the graphical package KiNG (Chen et al., 2009; Chapter 21.5), now included in PHENIX. Command ... 36. Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. ...

Structural coordinates and experimental data
Schneider, B., de la Cruz, J., Dutta, S., Feng, Z., Chen, L., Westbrook, J., Yang, H., Young, J., Zardecki, C. and Berman, H.M.  International Tables for Crystallography (2012). Vol. F, Section 24.2.4.1, p. 835 [ doi:10.1107/97809553602060000897 ]
Structural coordinates and experimental data 24.2.4.1. Structural coordinates and experimental data Structural coordinate files can be downloaded in mmCIF and PDB formats (Westbrook & Fitzgerald, 2009). Coordinates for the biological assembly of the molecule are provided for X-ray structures. When available, experimental files are made accessible to the community users. ...
     [more results from section 24.2.4 in volume F]

Atlas pages
Schneider, B., de la Cruz, J., Dutta, S., Feng, Z., Chen, L., Westbrook, J., Yang, H., Young, J., Zardecki, C. and Berman, H.M.  International Tables for Crystallography (2012). Vol. F, Section 24.2.3.4, p. 835 [ doi:10.1107/97809553602060000897 ]
Atlas pages 24.2.3.4. Atlas pages A powerful reporting option is the NDB Atlas (Fig. 24.2.3.1). An Atlas report summarizes the most important characteristics of a structure with information about the authors, citation, sequence(s) of nucleic acids and proteins reported. Atlas entries contain an outline of the experimental information, a ...
     [more results from section 24.2.3 in volume F]

Data processing and validation
Schneider, B., de la Cruz, J., Dutta, S., Feng, Z., Chen, L., Westbrook, J., Yang, H., Young, J., Zardecki, C. and Berman, H.M.  International Tables for Crystallography (2012). Vol. F, Section 24.2.2, pp. 833-834 [ doi:10.1107/97809553602060000897 ]
... Macromolecular Crystallographic Information File. Methods Enzymol. 277, 571-590. Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. ... pp. 144-198. Dordrecht: Springer. Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W. K. & Berman, H. M. (1996 ... Chem. Soc. 118, 519-528. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). ...

Introduction
Schneider, B., de la Cruz, J., Dutta, S., Feng, Z., Chen, L., Westbrook, J., Yang, H., Young, J., Zardecki, C. and Berman, H.M.  International Tables for Crystallography (2012). Vol. F, Section 24.2.1, p. 833 [ doi:10.1107/97809553602060000897 ]
... 10, 980. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan ...

The Nucleic Acid Database
Schneider, B., de la Cruz, J., Dutta, S., Feng, Z., Chen, L., Westbrook, J., Yang, H., Young, J., Zardecki, C. and Berman, H.M.  International Tables for Crystallography (2012). Vol. F, ch. 24.2, pp. 833-837 [ doi:10.1107/97809553602060000897 ]
... 10, 980. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan ... ray Crystallography and NMR. Version 3.1. Yale University, USA. Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. ... pp. 144-198. Dordrecht: Springer. Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W. K. & Berman, H. M. ( ...

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 ...

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 ]
... N. W., Zwart, P., Read, R. J., Turk, D. & Hung, L.-W. (2007). Interpretation of ensembles created by multiple iterative ...
     [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 ]
Ligand-coordinate and restraint-geometry generation 18.11.6.1. Ligand-coordinate and restraint-geometry generation The electronic Ligand Builder and Optimization Builder (eLBOW; Moriarty et al., 2009) is a suite of tools designed for the reliable generation of Cartesian coordinates and geometry restraints for both novel and known ligands. In line with the ...
     [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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