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PrimeX and the Schrödinger computational chemistry suite of programs
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, ch. 18.10, pp. 534-538 [ doi:10.1107/97809553602060000864 ]
... with real-space refinement and are ranked by real-space R factor. The top five poses for the ligand are returned ... attention. A density fit table (Fig.18.10.4.2) lists the real-space R factors for each main chain and side chain and for ... 2008). References Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Cross-validated ...

Validation
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.4.6, pp. 537-538 [ doi:10.1107/97809553602060000864 ]
... attention. A density fit table (Fig.18.10.4.2) lists the real-space R factors for each main chain and side chain and for ...
     [more results from section 18.10.4 in volume F]

Automation of refinement tasks
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.3.3, p. 536 [ doi:10.1107/97809553602060000864 ]
Automation of refinement tasks 18.10.3.3. Automation of refinement tasks As well as executing through the graphical interface, most PrimeX tasks can be run through command-line execution, so these tasks can be easily integrated into workflows. Future development will be focused on combining multiple tasks and diagnostic information into larger automated ...
     [more results from section 18.10.3 in volume F]

Molecular mechanics
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.2.3, p. 535 [ doi:10.1107/97809553602060000864 ]
... J. Am. Chem. Soc. 118, 11225-11236. Kaminski, G., Friesner, R. A., Tirado-Rives, J. & Jorgensen, W. L. (2001). Evaluation ...
     [more results from section 18.10.2 in volume F]

Implementation path
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.1.3, p. 534 [ doi:10.1107/97809553602060000864 ]
Implementation path 18.10.1.3. Implementation path In a field where most of the available software has been developed from academic sources, PrimeX is the only refinement program for biological crystallography that has been developed in a commercial environment. The advantage of commercial development includes high standards for consistency, professional software support and ...
     [more results from section 18.10.1 in volume F]

Conclusion
Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R.  International Tables for Crystallography (2012). Vol. F, Section 18.10.5, p. 538 [ doi:10.1107/97809553602060000864 ]
... J. L., Zhou, Z., Gallicchio, E., Himmel, D. M., Friesner, R. A., Arnold, E. & Levy, R. M. (2008). Exploring structural variability in X-ray ...

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