TNT refinement package.

By D. Tronrud. 1997

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, neutral): “The total model structure factor comprises a number of contributions, Fmodel ¼ koverall exp 2 2htUcrysth Fcalc þ ksol exp Bsols 2 4 Fmask ; ð1Þ where koverall is an overall scale factor, Ucryst is the overall anisotropic scale matrix (Sheriff & Hendrickson, 1987; Grosse-Kunstleve & Adams, 2002), h i”
Bulk-solvent and overall scaling revisited: faster calculations, improved results (2013, background): “Alternatives have been proposed (Tronrud, 1997; Vassylyev et al., 2007), but are not currently in wide use.”
Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. (2004, methodology): “TNT (Tronrud et al., 1987; Tronrud, 1992, 1996, 1997, 1999) receives the likelihood derivatives from BUSTER, evaluates the stereochemistry and NCS restraints residuals and their derivatives and shifts the coordinates, B factors and occupancies of the atomic model to maximize their likelihood while…”
Mechanisms of photoprotection and nonphotochemical quenching in pea light‐harvesting complex at 2.5 Å resolution (2005, methodology): “Maximum likelihood refinement and maximum entropy completion of the model (Tronrud, 1997; Roversi et al, 2000) allowed clear identification of the parts missing in the EM model and accelerated the process of refinement.”
Polder maps: improving OMIT maps by excluding bulk solvent (2017, methodology): “…in calculating OMIT maps, such as truncating the low-resolution data and not using the bulksolvent model at all, or using alternative bulk-solvent models that do not employ a priori modeling (masking), such as the exponential scaling (Babinet) model (Moews & Kretsinger, 1975; Tronrud, 1997).”
Flat bulk-solvent model: obtaining optimal parameters. (2002, background): “The exponential scaling model (Moews & Kretsinger, 1975; Tronrud, 1997) is based on the assumption that the structure factors of the solvent are proportional to those of the protein and have the opposite direction, Fsol s; sol; sol ÿ sol exp ÿ sols2=4 Fprot s : 1 [Here and in the following s…”
Averaged kick maps: less noise, more signal…and probably less bias (2009, methodology): “…correction models have been developed in order to be able to include all reflections in the map calculation rather than applying a low-resolution truncation (Moews & Kretsinger, 1975; Phillips, 1980; Jiang & Brünger, 1994; Tronrud, 1997; Badger, 1997; Urzhumtsev, 2000; Fokine & Urzhumtsev, 2002).”
SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. (1999, background): “A large d-spacing cutoff is usually applied to remove the in¯uence of disordered solvent molecules, which contribute to the diffraction at low nominal resolution (Tronrud, 1997).”
Crystal structures (2004, unknown): “Here, we use a slight modification of the formulation described by Tronrud (1997) and assume that if protein electron density is convoluted using the Gaussian kernel and multiplied by an appropriate scale factor, then protein and solvent electron densities are equal, solvent þFðkbabinetÞ protein ¼…”