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 Results for DC.creator="Y." AND DC.creator="Cao" in section 18.10.3 of 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 ...

Molecular models consistent with X-ray data
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 18.10.3.2, pp. 535-536 [ doi:10.1107/97809553602060000864 ]
Molecular models consistent with X-ray data 18.10.3.2. Molecular models consistent with X-ray data All current programs for refinement of biological crystal structures employ geometric restraints that either originate with or are consistent with a survey of small-molecule structures by Engh & Huber (1991). Other geometric restraints for group ...

van der Waals interactions
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 18.10.3.1.3, p. 535 [ doi:10.1107/97809553602060000864 ]
van der Waals interactions 18.10.3.1.3. van der Waals interactions The full OPLS force field includes terms for repulsive and attractive non-bonded interactions. Most significant for restraints during crystallographic refinement is the utilization of the full repulsive term for non-bonded interactions, unlike other leading biological crystal structure refinement packages where ...

Achieving the mission of PrimeX
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, pp. 535-536 [ doi:10.1107/97809553602060000864 ]
Achieving the mission of PrimeX 18.10.3. Achieving the mission of PrimeX The main goal of any X-ray crystal structure refinement program is to produce an optimized fit to the X-ray diffraction data, consistent with known molecular stereochemistry. For PrimeX, the additional goal is to include hydrogen atoms in the ...

Hydrogen atoms
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 18.10.3.1.1, p. 535 [ doi:10.1107/97809553602060000864 ]
Hydrogen atoms 18.10.3.1.1. Hydrogen atoms Although crystallographers have generally not included coordinates for hydrogen atoms in their models at moderate resolution, this situation has not always been so. During the early years of development of the very popular XPLOR package for refinement (Brünger, 1992), which was later augmented to become ...

Molecular models and computational chemistry
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 18.10.3.1, p. 535 [ doi:10.1107/97809553602060000864 ]
Molecular models and computational chemistry 18.10.3.1. Molecular models and computational chemistry 18.10.3.1.1. Hydrogen atoms | | Although crystallographers have generally not included coordinates for hydrogen atoms in their models at moderate resolution, this situation has not always been so. During the early years of development of the very popular XPLOR package for refinement ...

Electrostatics and implicit solvation
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 18.10.3.1.2, p. 535 [ doi:10.1107/97809553602060000864 ]
Electrostatics and implicit solvation 18.10.3.1.2. Electrostatics and implicit solvation For hydrogen atoms bonded to more electronegative atoms, electrostatic forces are a major determinant of non-bonded interactions, and they must be evaluated during the calculation of geometric gradients in the refinement. Thus, PrimeX employs the complete molecular mechanics description of atomic ...

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