Introduction to CC4i2¶
Tutorials from the CCP4i2 Roadshow¶
Experimental Phasing¶
Molecular replacement¶
- Programs
- Scenario
- Task 1: Run PHASER to position “Beta” and BLIP
- Task 2: Building the complex one component as a time.
- CCP4i2 Tutorial: Inhibitor-bound ternary complex of CDK1, Cyclin B1 and CKS2
- CCP4i2 MR Tutorial: Apo-CeuE (PDB:3ZKW)
- CCP4i2 MR Tutorial: Preparing AlphaFold/RoseTTAFold search models for MR. (Gamma example)
Ligands¶
- Programs
- Scenario
- Task 1: Get the data
- Task 2: Make your ligand – Make ligand task (LIDIA, ACEDRG, RDKIT)
- Task 3: Generate a starting model (Molecular replacement: PHASER)
- Task 4: Refine the starting model to create difference density for the ligand (Refinement: REFMAC5)
- Task 5: Generate a starting model (Manual model building: COOT, Refinement – REFMAC5)
- Task 6: Introduce your ligand into the structure (Manual model building: COOT)
- CCP4i2 Tutorial: Glyco (PDB:4IID)
- Programs
- Scenario
- Task 1: Data import – Import from Xia2
- Task 2: Ligand pipeline