sep_10_2019 - I2PC/scipion-courses GitHub Wiki

Course Material

• Presentation (Marta)

  • Scipion model building tutorial
  • PPT presentation (model building) (Marta)
  • Haemoglobin Movie
  • Poster (General model building workflow)

• 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)

  • Haemoglobin in PDB: ID 5ni1
    • Haemoglobin PDB full validation report

• Contacts AD type V (zhou)

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11:30 (PPT)

1. Introduction to Model building (Marta), present model building
2. Problem to solve: Haemoglobin (Marta), present tutorial data and aim 12:00

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1. Kahoot 000 (refresh key figures needed in the processing) SCIPION
2. Make sure ALL people open tutorial
3. Connection to amazon -> USE CABLE
4. Import volume and sequence data (Roberto) 13:00

14:00

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

16:30

1. extra tutorial coot (roberto)
2. Refinement: Flexible fitting (roberto), coot, refmac
3. real space refine (roberto)(tomorrow?) 18:30

9:00

1. Summary
2. Kahoot
3. Structure validation and comparison(Marta)(tomorrow?) validation cryoem, emringer
4. Create B subunit. (Marta)
5. Building the unit cell (Marta) use our very own beta
6. The whole macromolecule (Marta)
7. subtract pdb from model 1, EMDB deposition (Marta) 11:00

11:30

1. contacts (Roberto), show example from a paper
2. Superpose PDB
3. survey? 13:00

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