july_8_2019

Course Material

• Presentation (marta)

  • Scipion model building tutorial
  • PPT presentation (model building) (marta)
  • Haemoglobin Movie

• Import Data (roberto)

  • Kahoot Link
  • BlastP (search for homologues)
  • Human haemoglobin
    • 3D map: emd_3488.map, available directory Data
    • sequence:
      • alpha subunit: UniProt ID P69905 (Homologous sequences: P01958, P01948, P81023, P83134) link
      • beta subunit: UniProt ID P68871 (Homologous sequences: P02062, P02057, G1U9Q8, P83133) link
    • PDB reference: 1pbx (artic fish: Pagothenia) link

• Coot Tutorial (roberto)

  • 3D map
  • atomic model

• EMDB submission link (marta)

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1. Introduction to Model building marta, present model buildiong
2. Problem to solve: Hemoglobin marta, present tutorial data and aim

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SCIPION

1. Import Input data roberto

2. 3D Map preprocessing (sharpening, unit cell) roberto

3. Structure Prediction by Sequence Homology. Searching for Homologues (web site) roberto

4. Moving from sequence to atomic structure scenario chimera modeller (marta)

5. Merging 3D Maps and Atomic Structures: Rigid Fitting (marta)

6. extra emdb validation (marta)

7. extra tutorial coot (roberto)

8. Refinement: Flexible fitting (roberto), coot, refmac in each step validate

9. Structure validation and comparison(marta)

10. Subunidad beta (work by yourself) (marta)

11. Building the unit cell (marta)

12. The whole macromolecule (marta) contancts (marta)

13. encuesta?

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