Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.
BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coord...
| Main Authors: | , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
2004
|
| _version_ | 1826258320438067200 |
|---|---|
| author | Blanc, E Roversi, P Vonrhein, C Flensburg, C Lea, S Bricogne, G |
| author_facet | Blanc, E Roversi, P Vonrhein, C Flensburg, C Lea, S Bricogne, G |
| author_sort | Blanc, E |
| collection | OXFORD |
| description | BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone. |
| first_indexed | 2024-03-06T18:32:08Z |
| format | Journal article |
| id | oxford-uuid:0a01dc83-4af9-4c6c-b87b-03a8a24fff4b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T18:32:08Z |
| publishDate | 2004 |
| record_format | dspace |
| spelling | oxford-uuid:0a01dc83-4af9-4c6c-b87b-03a8a24fff4b2022-03-26T09:21:30ZRefinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:0a01dc83-4af9-4c6c-b87b-03a8a24fff4bEnglishSymplectic Elements at Oxford2004Blanc, ERoversi, PVonrhein, CFlensburg, CLea, SBricogne, GBUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone. |
| spellingShingle | Blanc, E Roversi, P Vonrhein, C Flensburg, C Lea, S Bricogne, G Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. |
| title | Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. |
| title_full | Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. |
| title_fullStr | Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. |
| title_full_unstemmed | Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. |
| title_short | Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. |
| title_sort | refinement of severely incomplete structures with maximum likelihood in buster tnt |
| work_keys_str_mv | AT blance refinementofseverelyincompletestructureswithmaximumlikelihoodinbustertnt AT roversip refinementofseverelyincompletestructureswithmaximumlikelihoodinbustertnt AT vonrheinc refinementofseverelyincompletestructureswithmaximumlikelihoodinbustertnt AT flensburgc refinementofseverelyincompletestructureswithmaximumlikelihoodinbustertnt AT leas refinementofseverelyincompletestructureswithmaximumlikelihoodinbustertnt AT bricogneg refinementofseverelyincompletestructureswithmaximumlikelihoodinbustertnt |