Session 1: Capsid molecular model from cryoEM map (White lab)
Recorded zoom session
Agenda
Part 1: Model building
Brief overview of maps:
Mention differences between cryoEM and crystallography (one is where the map is the data and the other you need to solve the structure). I would only focus on cryoEM maps. Mention it is probably worth using Isolde to re-refine existing cryoEM structures. Probably not worth it for structures worse than 4 Angstrom.
Talk about where to get raw data from if you want to re-do the whole analysis (might be worthwhile for older data sets). Talk about EMDB and EMPIAR. Won’t discuss data analysis here but happy to have one-on-one sessions to teach people.
Talk about phenix and CCPEM and the sharpening of cryoEM maps. CCPEM is a pain to install on mac. Also can’t handle the very large maps.
Map preparation for model building:
- Brief overview of model building
- Show chimera and chimerax.
- Show coot. Show how to get Oli Clarke trimmings.
- Run through model building on coot. Talk about asymmetric unit
Talk about using alphafold/ITasser/Phyre2 to make an initial model or de novo.
Parts 2 and 3: Model refinement
- Use coot to start refine
- Use phenix for refinement
- Use Isolde for refinement
- Use PDB validation server for final checking: Need to show an image of amino acid with C alpha and C beta.