All Stories

  1. Universal parameters of bulk-solvent masks
  2. Overall protein structure quality assessment using hydrogen-bonding parameters
  3. Efficient structure-factor modeling for crystals with multiple components
  4. Bulk-solvent and overall scaling revisited: faster calculations, improved results. Corrigendum.
  5. New tools for the analysis and validation of cryo-EM maps and atomic models
  6. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
  7. Real-space refinement inPHENIXfor cryo-EM and crystallography
  8. Solving the scalability issue in quantum-based refinement: Q|R#1
  9. FEM: feature-enhanced map
  10. From deep TLS validation to ensembles of atomic models built from elemental motions
  11. Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles
  12. Metrics for comparison of crystallographic maps
  13. Virus model of brome mosaic virus (second half data set)
  14. Full virus map of brome mosaic virus
  15. Virus model of brome mosaic virus (first half data set)
  16. An atomic model of brome mosaic virus using direct electron detection and real-space optimization
  17. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement
  18. Automated identification of elemental ions in macromolecular crystal structures
  19. Automating crystallographic structure solution and refinement of protein–ligand complexes
  20. Improved Crystallographic Structures Using Extensive Combinatorial Refinement
  21. Model morphing and sequence assignment after molecular replacement
  22. TLSfrom fundamentals to practice
  23. Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling
  24. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling
  25. Bulk-solvent and overall scaling revisited: faster calculations, improved results
  26. Crystallographic Maps and Models at Low and at Subatomic Resolutions
  27. Crystallographic Structure Refinement in a Nutshell
  28. Modelling dynamics in protein crystal structures by ensemble refinement
  29. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement
  30. Graphical tools for macromolecular crystallography inPHENIX
  31. PHENIX: a comprehensive Python-based system for macromolecular structure solution
  32. Towards automated crystallographic structure refinement with phenix.refine
  33. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution
  34. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta
  35. The Phenix software for automated determination of macromolecular structures
  36. N-{N-[2-(3,5-Difluorophenyl)acetyl]-(S)-alanyl}-(S)-phenylglycinetert-butyl ester (DAPT): an inhibitor of γ-secretase, revealing fine electronic and hydrogen-bonding features
  37. Joint X-ray and neutron refinement withphenix.refine
  38. Coupling of receptor conformation and ligand orientation determine graded activity
  39. Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles
  40. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics
  41. Neutron Diffraction Studies of a Class A β-Lactamase Toho-1 E166A/R274N/R276N Triple Mutant
  42. PHENIX: a comprehensive Python-based system for macromolecular structure solution
  43. On the use of logarithmic scales for analysis of diffraction data
  44. Recent developments in phasing and structure refinement for macromolecular crystallography
  45. Averaged kick maps: less noise, more signal…and probably less bias
  46. Automatic multiple-zone rigid-body refinement with a large convergence radius
  47. Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
  48. Decision-making in structure solution using Bayesian estimates of map quality: thePHENIX AutoSolwizard
  49. Crystallographic model quality at a glance
  50. Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias
  51. Protein structures by spallation neutron crystallography
  52. Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase
  53. Automated Structure Solution with the PHENIX Suite
  54. Iterative model building, structure refinement and density modification with thePHENIX AutoBuildwizard
  55. On macromolecular refinement at subatomic resolution with interatomic scatterers
  56. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
  57. Automated structure determination with phenix
  58. A robust bulk solvent correction and anisotropic scaling procedure in the CCTBX
  59. On the incompleteness of atomic models
  60. Hybrid programming in crystallography: Phenix.refine and Phenix.hyss
  61. A robust bulk-solvent correction and anisotropic scaling procedure
  62. Some Applications of Dummy Point Scatterers for Phasing in Macromolecular X-Ray Crystallography
  63. On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps
  64. On a fast calculation of structure factors at a subatomic resolution
  65. MLMF: least-squares approximation of likelihood-based refinement criteria
  66. Quadratic approximation of the maximum-likelihood criterion
  67. Likelihood-based refinement. I. Irremovable model errors