Model Building Tutorial

This tutorial shows a workflow aimed at obtaining high-quality atomic models from cryo-EM data by using scipion software framework.

Contents

• 1. Revision History
• 2. Prelude
• 3. Introduction to Model building
• 4. Problem to solve: Haemoglobin
• 5. Input data description
• 6. Import Input data
• 7. 3D Map preprocessing
• 8. Structure Prediction by Sequence Homology. Searching for Homologues
• 9. Moving from sequence to atomic structure scenario
• 10. Merging 3D Maps and Atomic Structures: Rigid Fitting
• 11. Refinement: Flexible fitting
• 12. Structure validation and comparison
• 13. Building the asymmetric unit
• 14. The whole macromolecule
• 15. Summary of results and submission
• 16. A Note on Software Installation
• 17. How to solve some problems that you can find during the execution of the modeling workflow
• 18. TODO
• 19. References

Appendices

• 1. Answers to Questions
• 2. Atomic Structure Chain Operator protocol
• 3. ChimeraX Contacts protocol
• 4. ChimeraX Map Subtraction protocol
• 5. ChimeraX Operate protocol
• 6. ChimeraX Restore Session protocol
• 7. ChimeraX Rigid Fit protocol
• 8. CCP4 Coot Refinement protocol
• 9. CCP4 Refmac protocol
• 10. Create 3D Mask protocol
• 11. DeepEMhancer Sharpening protocol
• 12. Extract asymmetric unit protocol
• 13. Import atomic structure protocol
• 14. Import sequence protocol
• 15. Import mask protocol
• 16. Import volume protocol
• 17. Local Deblur Sharpening protocol
• 18. Local MonoRes protocol
• 19. Model from Template protocol
• 20. Phenix EMRinger protocol
• 21. Phenix MolProbity protocol
• 22. Phenix Validation CryoEM protocol
• 23. Phenix Real Space Refine protocol
• 24. Phenix Superpose PDBs protocol
• 25. Phenix Dock in Map protocol
• 26. Phenix Search Fit protocol
• 27. Protocol to assign map sampling rate and origin of coordinates
• 28. Submission to wwPDB protocol