sep_10_2019 - I2PC/scipion-courses GitHub Wiki
Course Material
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Presentation (Marta)
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Import Data (Roberto)
- Kahoot Link
- BlastP (search for homologues)
- Human haemoglobin
- 3D map: emd_3488.map, available directory Data
- sequence:
- PDB reference: 1pbx (antartic fish: Pagothenia bernacchii) link
-
Coot Tutorial (Roberto)
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EMDB submission link (Marta)
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11:30 (PPT)
- Introduction to Model building (Marta), present model building
- Problem to solve: Haemoglobin (Marta), present tutorial data and aim 12:00
- Kahoot 000 (refresh key figures needed in the processing) SCIPION
- Make sure ALL people open tutorial
- Connection to amazon -> USE CABLE
- Import volume and sequence data (Roberto) 13:00
14:00
- 3D Map preprocessing (create mask, sharpening, unit cell) (monores, sharpening) (Roberto)
- Structure Prediction by Sequence Homology. Searching for Homologues (web site) (Roberto)
- import reference atom struct (roberto) 15:00
- Moving from sequence to atomic structure scenario chimera modeller (Marta)
- Merging 3D Maps and Atomic Structures: Rigid Fitting (Marta)
- kahoot 200 (marta) 16:00
16:30
- extra tutorial coot (roberto)
- Refinement: Flexible fitting (roberto), coot, refmac
- real space refine (roberto)(tomorrow?) 18:30
9:00
- Summary
- Kahoot
- Structure validation and comparison(Marta)(tomorrow?) validation cryoem, emringer
- Create B subunit. (Marta)
- Building the unit cell (Marta) use our very own beta
- The whole macromolecule (Marta)
- subtract pdb from model 1, EMDB deposition (Marta) 11:00
11:30
- contacts (Roberto), show example from a paper
- Superpose PDB
- survey? 13:00
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