july_8_2019 - I2PC/scipion-courses GitHub Wiki

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 (antartic fish: Pagothenia bernacchii) link

• Coot Tutorial (Roberto)

  • 3D map
  • atomic model

• EMDB submission link (Marta)

====== 11:00

1. Introduction to Model building (Marta), present model building
2. Problem to solve: Hemoglobin (Marta), present tutorial data and aim 11:30

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1. Kahoot 000 SCIPION
2. Import volume and sequence data (Roberto)
3. 3D Map preprocessing (sharpening, unit cell) (Roberto) 13:00

14:00

1. Structure Prediction by Sequence Homology. Searching for Homologues (web site) (Roberto)
2. import reference atom struct 1, kahoot 100 15:00
3. Moving from sequence to atomic structure scenario chimera modeller (Marta)
4. Merging 3D Maps and Atomic Structures: Rigid Fitting (Marta)
5. kahoot 200 16:00

16:30

1. extra tutorial coot (Roberto)
2. Refinement: Flexible fitting (Roberto), coot, refmac in each step validate (refmac if needed)
3. real space refine (tomorrow?)
4. Structure validation and comparison(Marta)(tomorrow?) 18:30

9:00

1. Building the unit cell (Marta) use our very own beta
2. The whole macromolecule (Marta) 1, EMDB (Marta) 11:00

11:30

1. contacts (Roberto)
2. Subunidad beta (work by yourself)
3. survey? 13:00

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