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PrimeX implementation and theory
International Tables for Crystallography (2012). Vol. F, Section 18.10.4, pp. 536-538 [ doi:10.1107/97809553602060000864 ]
PrimeX implementation and theory 18.10.4. PrimeX implementation and theory 18.10.4.1. Force-field model and automatic atom typing | | An important feature of PrimeX is that all molecules are automatically treated with atom typing and parameters are generated without the intervention of the crystallographer. This capability saves a large amount of time that ...
Ligand placement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.5, p. 537 [ doi:10.1107/97809553602060000864 ]
Ligand placement 18.10.4.5. Ligand placement Ligand placement can be accessed through a convenient GUI (Fig.18.10.4.1). The algorithm for ligand placement was derived from the docking program Glide (Friesner et al., 2004). In brief, the program abstracts the protein model as an energy grid in which the properties of the ...
Water placement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.4, p. 537 [ doi:10.1107/97809553602060000864 ]
Water placement 18.10.4.4. Water placement Waters may be added by PrimeX to difference electron-density maps for positive peaks exceeding a selected level of significance. Prospective water sites in the electron-density map are screened by three different criteria related to distance from other atoms. Water molecules that refine to a ...
Minimization
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.3, p. 537 [ doi:10.1107/97809553602060000864 ]
Minimization 18.10.4.3.3. Minimization Real-space minimization provides an additional method of optimizing model coordinates according to the electron density and force field, as well as playing an integral part in the building of polypeptide chains, the placement of amino-acid side chains and the placement of ligands. References International Tables for ...
Side-chain placement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.2, p. 537 [ doi:10.1107/97809553602060000864 ]
Side-chain placement 18.10.4.3.2. Side-chain placement Also based on Prime technology, one or multiple side chains may be simultaneously evaluated and placed into electron density. Even if two side chains have overlapping conformations at the start of the process, they will both be placed into appropriate electron density. As an ...
Loop refinement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.1, p. 537 [ doi:10.1107/97809553602060000864 ]
Loop refinement 18.10.4.3.1. Loop refinement Polypeptide segments, both internal (loops) and external (tails), can be built from the target sequence as stored in the program. The program builds polypeptides according to an algorithm derived from the protein-modelling program Prime (Jacobson et al., 2004; Zhu, Shirts & Friesner, 2007). Using the ...
Real-space tools
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3, p. 537 [ doi:10.1107/97809553602060000864 ]
Real-space tools 18.10.4.3. Real-space tools 18.10.4.3.1. Loop refinement | | Polypeptide segments, both internal (loops) and external (tails), can be built from the target sequence as stored in the program. The program builds polypeptides according to an algorithm derived from the protein-modelling program Prime (Jacobson et al., 2004; Zhu, Shirts ...
Omit maps
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.4, pp. 536-537 [ doi:10.1107/97809553602060000864 ]
Omit maps 18.10.4.2.4. Omit maps Omit maps (Bhat & Cohen, 1984; Bhat, 1988) have been implemented because of their demonstrated ability to reduce model-derived bias in maps (Vellieux & Dijkstra, 1997). The kicked omit maps described by Guncar et al. (2000) have also been included in PrimeX. After all the atoms ...
Map generation
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.3, p. 536 [ doi:10.1107/97809553602060000864 ]
Map generation 18.10.4.2.3. Map generation Map calculations in PrimeX are based on the sigmaA weighting scheme of Read (1986), a data treatment that has been shown to decrease the bias in electron-density maps. Optionally, an unweighted map may be calculated. References Read, R. J. (1986). Improved Fourier coefficients for ...
Simulated annealing
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.2, p. 536 [ doi:10.1107/97809553602060000864 ]
Simulated annealing 18.10.4.2.2. Simulated annealing Simulated-annealing refinement was implemented within the general-purpose molecular modelling package IMPACT (Banks et al., 2005), employing concepts for simulated-annealing refinement validated in the program CNS (Adams et al., 1997). PrimeX simulated annealing provides two alternative energy models for dynamic simulation refinement. In ...
International Tables for Crystallography (2012). Vol. F, Section 18.10.4, pp. 536-538 [ doi:10.1107/97809553602060000864 ]
PrimeX implementation and theory 18.10.4. PrimeX implementation and theory 18.10.4.1. Force-field model and automatic atom typing | | An important feature of PrimeX is that all molecules are automatically treated with atom typing and parameters are generated without the intervention of the crystallographer. This capability saves a large amount of time that ...
Ligand placement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.5, p. 537 [ doi:10.1107/97809553602060000864 ]
Ligand placement 18.10.4.5. Ligand placement Ligand placement can be accessed through a convenient GUI (Fig.18.10.4.1). The algorithm for ligand placement was derived from the docking program Glide (Friesner et al., 2004). In brief, the program abstracts the protein model as an energy grid in which the properties of the ...
Water placement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.4, p. 537 [ doi:10.1107/97809553602060000864 ]
Water placement 18.10.4.4. Water placement Waters may be added by PrimeX to difference electron-density maps for positive peaks exceeding a selected level of significance. Prospective water sites in the electron-density map are screened by three different criteria related to distance from other atoms. Water molecules that refine to a ...
Minimization
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.3, p. 537 [ doi:10.1107/97809553602060000864 ]
Minimization 18.10.4.3.3. Minimization Real-space minimization provides an additional method of optimizing model coordinates according to the electron density and force field, as well as playing an integral part in the building of polypeptide chains, the placement of amino-acid side chains and the placement of ligands. References International Tables for ...
Side-chain placement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.2, p. 537 [ doi:10.1107/97809553602060000864 ]
Side-chain placement 18.10.4.3.2. Side-chain placement Also based on Prime technology, one or multiple side chains may be simultaneously evaluated and placed into electron density. Even if two side chains have overlapping conformations at the start of the process, they will both be placed into appropriate electron density. As an ...
Loop refinement
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3.1, p. 537 [ doi:10.1107/97809553602060000864 ]
Loop refinement 18.10.4.3.1. Loop refinement Polypeptide segments, both internal (loops) and external (tails), can be built from the target sequence as stored in the program. The program builds polypeptides according to an algorithm derived from the protein-modelling program Prime (Jacobson et al., 2004; Zhu, Shirts & Friesner, 2007). Using the ...
Real-space tools
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.3, p. 537 [ doi:10.1107/97809553602060000864 ]
Real-space tools 18.10.4.3. Real-space tools 18.10.4.3.1. Loop refinement | | Polypeptide segments, both internal (loops) and external (tails), can be built from the target sequence as stored in the program. The program builds polypeptides according to an algorithm derived from the protein-modelling program Prime (Jacobson et al., 2004; Zhu, Shirts ...
Omit maps
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.4, pp. 536-537 [ doi:10.1107/97809553602060000864 ]
Omit maps 18.10.4.2.4. Omit maps Omit maps (Bhat & Cohen, 1984; Bhat, 1988) have been implemented because of their demonstrated ability to reduce model-derived bias in maps (Vellieux & Dijkstra, 1997). The kicked omit maps described by Guncar et al. (2000) have also been included in PrimeX. After all the atoms ...
Map generation
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.3, p. 536 [ doi:10.1107/97809553602060000864 ]
Map generation 18.10.4.2.3. Map generation Map calculations in PrimeX are based on the sigmaA weighting scheme of Read (1986), a data treatment that has been shown to decrease the bias in electron-density maps. Optionally, an unweighted map may be calculated. References Read, R. J. (1986). Improved Fourier coefficients for ...
Simulated annealing
International Tables for Crystallography (2012). Vol. F, Section 18.10.4.2.2, p. 536 [ doi:10.1107/97809553602060000864 ]
Simulated annealing 18.10.4.2.2. Simulated annealing Simulated-annealing refinement was implemented within the general-purpose molecular modelling package IMPACT (Banks et al., 2005), employing concepts for simulated-annealing refinement validated in the program CNS (Adams et al., 1997). PrimeX simulated annealing provides two alternative energy models for dynamic simulation refinement. In ...
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