sep_17_2019 - I2PC/scipion-courses GitHub Wiki

Course Material

• Presentation

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

• Import Data

  • 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

  • 3D map
  • atomic model

• EMDB submission link

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

• Contacts AD type V (Zhou)

======

16:30 (PPT)

1. Introduction to Model building, present model building
2. Problem to solve: Haemoglobin, present tutorial data and aim
3. Kahoot 000 (refresh key figures needed in the processing)
4. Make sure ALL people open tutorial
5. Connection to amazon -> USE CABLE
6. Import volume in SCIPION
7. 3D Map preprocessing (create mask, sharpening, unit cell) (monores, sharpening)

---

9:00

1. Import sequence in SCIPION
2. import reference atom struct
3. Structure Prediction by Sequence Homology. Searching for Homologues (web site)
4. Moving from sequence to atomic structure scenario chimera modeller

---

11:00

1. Merging 3D Maps and Atomic Structures: Rigid Fitting
2. Refinement: Flexible fitting, coot, refmac, real space refine
3. kahoot 200

---

14:00

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

---

16:30

1. contacts (Roberto), show example from a paper
2. Superpose PDB
3. survey? 18:00

====