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Results for DC.creator="D." AND DC.creator="E." AND DC.creator="Tronrud" in section 18.7.5 of volume F |
Innovations first introduced in TNT
International Tables for Crystallography (2012). Vol. F, Section 18.7.5, pp. 522-523 [ doi:10.1107/97809553602060000861 ]
... of the scattering of the bulk solvent in the crystal (Tronrud, 1997), the low-resolution data could be used in refinement ... gradient minimization (1990) | | This method of minimization (Axelsson & Barker, 1984; Tronrud, 1992) allows the direct inclusion of the diagonal elements of ... the traditional restraint is flawed. A restraint library was generated (Tronrud, 1996) where each bond in a residue is assigned ...
Block-diagonal preconditioned conjugate-gradient minimization with pseudoinverses (1998)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.8, p. 523 [ doi:10.1107/97809553602060000861 ]
Block-diagonal preconditioned conjugate-gradient minimization with pseudoinverses (1998) 18.7.5.8. Block-diagonal preconditioned conjugate-gradient minimization with pseudoinverses (1998) With this enhancement, TNT's minimizer treats the second-derivative matrix as a collection of 5 × 5 element blocks along its diagonal, one block for each atom. While this method improves the ...
Knowledge-based B-factor restraints (~1994)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.7, pp. 522-523 [ doi:10.1107/97809553602060000861 ]
... the traditional restraint is flawed. A restraint library was generated (Tronrud, 1996) where each bond in a residue is assigned a ... factor and a confidence (standard deviation) in that increment. References Tronrud, D. E. (1996). Knowledge-based B-factor restraints for ...
Restraining stereochemistry of chemical links to symmetry-related molecules (~1992)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.6, p. 522 [ doi:10.1107/97809553602060000861 ]
Restraining stereochemistry of chemical links to symmetry-related molecules (~1992) 18.7.5.6. Restraining stereochemistry of chemical links to symmetry-related molecules (~1992) It is not uncommon for crystallization enhancers to be found on a special position in the crystal. In addition, cross-linking the molecules in a crystal is often done for ...
Preconditioned conjugate-gradient minimization (1990)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.5, p. 522 [ doi:10.1107/97809553602060000861 ]
... gradient minimization (1990) This method of minimization (Axelsson & Barker, 1984; Tronrud, 1992) allows the direct inclusion of the diagonal elements of ... value problems, ch. 1, pp. 1-63. Orlando: Academic Press. Tronrud, D. E. (1992). Conjugate-direction minimization: an improved method ...
Modelling bulk solvent scattering via local scaling (~1989)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.4, p. 522 [ doi:10.1107/97809553602060000861 ]
... of the scattering of the bulk solvent in the crystal (Tronrud, 1997), the low-resolution data could be used in refinement ... in the calculation of maps greatly improved their appearance. References Tronrud, D. E. (1997). TNT refinement package. Methods Enzymol. 277, ...
Space-group optimized FFTs for all space groups (1989)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.3, p. 522 [ doi:10.1107/97809553602060000861 ]
Space-group optimized FFTs for all space groups (1989) 18.7.5.3. Space-group optimized FFTs for all space groups (1989) This innovation allowed TNT to run efficiently in all space groups available to macromolecular crystals. References International Tables for Crystallography (2012). Vol. F, ch. 18.7, p. 522 © International Union of Crystallography ...
The ability of a single package to perform both individual atom and rigid-body refinement (1982)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.2, p. 522 [ doi:10.1107/97809553602060000861 ]
The ability of a single package to perform both individual atom and rigid-body refinement (1982) 18.7.5.2. The ability of a single package to perform both individual atom and rigid-body refinement (1982) Prior to TNT, one often started a refinement with rigid-body refinement using CORELS and then switched to ...
Identifying and restraining symmetry-related contacts (1982)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.1, p. 522 [ doi:10.1107/97809553602060000861 ]
Identifying and restraining symmetry-related contacts (1982) 18.7.5.1. Identifying and restraining symmetry-related contacts (1982) Without a search for symmetry-related bad contacts, it was quite common to build atoms into the same density from two different sides of the molecule. A number of models in the Protein Data Bank contain ...
Generalization of noncrystallographic symmetry operators to include shifts in the average B factor (1998)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.9, p. 523 [ doi:10.1107/97809553602060000861 ]
Generalization of noncrystallographic symmetry operators to include shifts in the average B factor (1998) 18.7.5.9. Generalization of noncrystallographic symmetry operators to include shifts in the average B factor (1998) It is rather common in crystals containing multiple copies of a molecule in the asymmetric unit for one or more molecules to ...
International Tables for Crystallography (2012). Vol. F, Section 18.7.5, pp. 522-523 [ doi:10.1107/97809553602060000861 ]
... of the scattering of the bulk solvent in the crystal (Tronrud, 1997), the low-resolution data could be used in refinement ... gradient minimization (1990) | | This method of minimization (Axelsson & Barker, 1984; Tronrud, 1992) allows the direct inclusion of the diagonal elements of ... the traditional restraint is flawed. A restraint library was generated (Tronrud, 1996) where each bond in a residue is assigned ...
Block-diagonal preconditioned conjugate-gradient minimization with pseudoinverses (1998)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.8, p. 523 [ doi:10.1107/97809553602060000861 ]
Block-diagonal preconditioned conjugate-gradient minimization with pseudoinverses (1998) 18.7.5.8. Block-diagonal preconditioned conjugate-gradient minimization with pseudoinverses (1998) With this enhancement, TNT's minimizer treats the second-derivative matrix as a collection of 5 × 5 element blocks along its diagonal, one block for each atom. While this method improves the ...
Knowledge-based B-factor restraints (~1994)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.7, pp. 522-523 [ doi:10.1107/97809553602060000861 ]
... the traditional restraint is flawed. A restraint library was generated (Tronrud, 1996) where each bond in a residue is assigned a ... factor and a confidence (standard deviation) in that increment. References Tronrud, D. E. (1996). Knowledge-based B-factor restraints for ...
Restraining stereochemistry of chemical links to symmetry-related molecules (~1992)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.6, p. 522 [ doi:10.1107/97809553602060000861 ]
Restraining stereochemistry of chemical links to symmetry-related molecules (~1992) 18.7.5.6. Restraining stereochemistry of chemical links to symmetry-related molecules (~1992) It is not uncommon for crystallization enhancers to be found on a special position in the crystal. In addition, cross-linking the molecules in a crystal is often done for ...
Preconditioned conjugate-gradient minimization (1990)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.5, p. 522 [ doi:10.1107/97809553602060000861 ]
... gradient minimization (1990) This method of minimization (Axelsson & Barker, 1984; Tronrud, 1992) allows the direct inclusion of the diagonal elements of ... value problems, ch. 1, pp. 1-63. Orlando: Academic Press. Tronrud, D. E. (1992). Conjugate-direction minimization: an improved method ...
Modelling bulk solvent scattering via local scaling (~1989)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.4, p. 522 [ doi:10.1107/97809553602060000861 ]
... of the scattering of the bulk solvent in the crystal (Tronrud, 1997), the low-resolution data could be used in refinement ... in the calculation of maps greatly improved their appearance. References Tronrud, D. E. (1997). TNT refinement package. Methods Enzymol. 277, ...
Space-group optimized FFTs for all space groups (1989)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.3, p. 522 [ doi:10.1107/97809553602060000861 ]
Space-group optimized FFTs for all space groups (1989) 18.7.5.3. Space-group optimized FFTs for all space groups (1989) This innovation allowed TNT to run efficiently in all space groups available to macromolecular crystals. References International Tables for Crystallography (2012). Vol. F, ch. 18.7, p. 522 © International Union of Crystallography ...
The ability of a single package to perform both individual atom and rigid-body refinement (1982)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.2, p. 522 [ doi:10.1107/97809553602060000861 ]
The ability of a single package to perform both individual atom and rigid-body refinement (1982) 18.7.5.2. The ability of a single package to perform both individual atom and rigid-body refinement (1982) Prior to TNT, one often started a refinement with rigid-body refinement using CORELS and then switched to ...
Identifying and restraining symmetry-related contacts (1982)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.1, p. 522 [ doi:10.1107/97809553602060000861 ]
Identifying and restraining symmetry-related contacts (1982) 18.7.5.1. Identifying and restraining symmetry-related contacts (1982) Without a search for symmetry-related bad contacts, it was quite common to build atoms into the same density from two different sides of the molecule. A number of models in the Protein Data Bank contain ...
Generalization of noncrystallographic symmetry operators to include shifts in the average B factor (1998)
International Tables for Crystallography (2012). Vol. F, Section 18.7.5.9, p. 523 [ doi:10.1107/97809553602060000861 ]
Generalization of noncrystallographic symmetry operators to include shifts in the average B factor (1998) 18.7.5.9. Generalization of noncrystallographic symmetry operators to include shifts in the average B factor (1998) It is rather common in crystals containing multiple copies of a molecule in the asymmetric unit for one or more molecules to ...
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