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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.

Part 4: Overtime/questions/discussion/prolate


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