International Tables for Crystallography (2012). Vol. F, ch. 18.10, pp. 534-538
doi: 10.1107/97809553602060000864

Chapter 18.10. PrimeX and the Schrödinger computational chemistry suite of programs

Contents

  • 18.10. PrimeX and the Schrödinger computational chemistry suite of programs   (pp. 534-538) | html | pdf | chapter contents |
    • 18.10.1. Introduction  (p. 534) | html | pdf |
      • 18.10.1.1. Computational environment  (p. 534) | html | pdf |
      • 18.10.1.2. Mission  (p. 534) | html | pdf |
      • 18.10.1.3. Implementation path  (p. 534) | html | pdf |
    • 18.10.2. Computational environment  (pp. 534-535) | html | pdf |
      • 18.10.2.1. Molecular graphics  (p. 534) | html | pdf |
      • 18.10.2.2. Supporting infrastructure  (p. 534) | html | pdf |
      • 18.10.2.3. Molecular mechanics  (p. 535) | html | pdf |
    • 18.10.3. Achieving the mission of PrimeX   (pp. 535-536) | html | pdf |
      • 18.10.3.1. Molecular models and computational chemistry  (p. 535) | html | pdf |
        • 18.10.3.1.1. Hydrogen atoms  (p. 535) | html | pdf |
        • 18.10.3.1.2. Electrostatics and implicit solvation  (p. 535) | html | pdf |
        • 18.10.3.1.3. van der Waals interactions  (p. 535) | html | pdf |
      • 18.10.3.2. Molecular models consistent with X-ray data  (pp. 535-536) | html | pdf |
      • 18.10.3.3. Automation of refinement tasks  (p. 536) | html | pdf |
    • 18.10.4. PrimeX implementation and theory  (pp. 536-538) | html | pdf |
      • 18.10.4.1. Force-field model and automatic atom typing  (p. 536) | html | pdf |
      • 18.10.4.2. Reciprocal-space calculations  (pp. 536-537) | html | pdf |
        • 18.10.4.2.1. Restrained maximum-likelihood minimization  (p. 536) | html | pdf |
        • 18.10.4.2.2. Simulated annealing  (p. 536) | html | pdf |
        • 18.10.4.2.3. Map generation  (p. 536) | html | pdf |
        • 18.10.4.2.4. Omit maps  (pp. 536-537) | html | pdf |
      • 18.10.4.3. Real-space tools  (p. 537) | html | pdf |
        • 18.10.4.3.1. Loop refinement  (p. 537) | html | pdf |
        • 18.10.4.3.2. Side-chain placement  (p. 537) | html | pdf |
        • 18.10.4.3.3. Minimization  (p. 537) | html | pdf |
      • 18.10.4.4. Water placement  (p. 537) | html | pdf |
      • 18.10.4.5. Ligand placement  (p. 537) | html | pdf |
      • 18.10.4.6. Validation  (pp. 537-538) | html | pdf |
    • 18.10.5. Conclusion  (p. 538) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 18.10.2.1. The project table entries track the steps of this refinement in progress  (p. 535) | html | pdf |
      • Fig. 18.10.3.1. The hydrogen-bond network optimizer clusters hydrogen-bond donors and acceptors to group together those that could possibly interact, so that these interactions can be efficiently optimized  (p. 536) | html | pdf |
      • Fig. 18.10.4.1. The ligand/solvent placement GUI provides a list of electron-density blobs from a map with coefficients F o  −  F c , together with their volume, and several ways to specify the molecules to be placed into the electron density  (p. 537) | html | pdf |
      • Fig. 18.10.4.2. The density fit table provides a convenient method for finding residues where the main chain or side chain in the model poorly fits the electron density  (p. 538) | html | pdf |
    • Tables
      • Table 18.10.1.1. Schrödinger software packages related to PrimeX   (p. 534) | html | pdf |