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Skeleton Secondary Structure Templates Directionality Sequence placement Complete model

O. Skeleton Secondary Structure Templates Directionality Sequence placement Complete model. Flowchart of model building with O. Map Skeleton New Skeleton Framework New Framework. In O, choose level. Essens, 2ry stru. Edit. Interactive or Sprout. Directionality, a -helix.

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Skeleton Secondary Structure Templates Directionality Sequence placement Complete model

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  1. O • Skeleton • Secondary Structure Templates • Directionality • Sequence placement • Complete model

  2. Flowchart of model building with O Map Skeleton New Skeleton Framework New Framework In O, choose level Essens, 2ry stru Edit Interactive or Sprout Directionality,a-helix Sequence placement Dejavu

  3. Extend placement Between SSTs build_ed_loop From 1 SST grab_build

  4. Use Skeletons • Compact data-structure • Provides an overview • Loss of detail (contour the map for detail) • Determine molecular boundary • Color to indicate trace

  5. Algorithm by J.Greer (1974) J.Mol.Biol.

  6. Edit skeleton • Errors in phases,mobility… • False connection • Main-chain hydrogen bonds • Interacting side-chains • SS bridges • Ligands..

  7. ESSENS Kleywegt & Jones (1997) Acta Cryst. D53, 179-185

  8. SSTs: alph9 alph7 beta7 beta5 RNA5 ESSENS Kleywegt & Jones (1997) Acta Cryst. D53, 179-185

  9. Complete Template Framework

  10. Chain directionality • Peptide branching, the distance Cai-Ci is much shorter than the distance Ci-Cai+1 • need good resolution (~2.5A or better) and good phases

  11. Chain directionality • At lower resolution use the helical Christmas tree affect. Local averaging can help. • Given a moderately well fitting helix, determine the operators from the central residue in the helix to each residue. Using these operators we can average the local density around the central residue with the density at each residue in the helix.

  12. Directionality Helix Christmas Tree Side-chains Point to N- Terminus of helix a1

  13. a2

  14. Extend directionality

  15. <<<

  16. In phase In phase

  17. In phase

  18. Out of phase

  19. Reversed, now in phase with next strand

  20. Until, finally the last b-strand

  21. Now we have a complete structural framework with the directionality in phase. Now for the sequence.

  22. Use DEJAVU to find related structures

  23. Sequence placement • Special side chains (e.g. aromatics) • Ligands • SeMet • Active site information

  24. Build_show

  25. The sequence slider

  26. Start at a1. Look at the bumps.

  27. The Slider commands

  28. Build_guess onto the framework New implementation of Zou & Jones (1996) Acta Cryst. D52 833-841 Test residues/rotamers. Build mask from backbone and ED level. Simple GFI in ED; fast. Makes a guess in Slider.

  29. Build_slider Real-time sliding

  30. Seconds to fit >>

  31. >>

  32. Then build the connections …

  33. Grab_build

  34. Various grow modes

  35. Various manip. commands

  36. * * Remains interactive at the moment, but …

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