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And ultimately you can try to improve your structure results by studying and applying the options available within the FLYA and noeassign modules of CYANA.
ContentsContent- 1 CYANA setup
- 2 Automated resonance assignment
- 2.1 Experimental input data
- 2.1.1 SPECTRUM definitions in the CYANA library
- 2.2 Exercise 1: Determine the spectrum type
- 2.3 Exercise 2: Run FLYA
- 2.3.1 Execution scripts or "macros" in CYANA
- 2.3.2 The init macro
- 2.3.3 The FLYA CALC macro
- 2.4 FLYA output files
- 2.4.1 The flya.txt file
- 2.4.2 The flya.tab file
- 2.4.3 The flya.pdf file
- 2.5 Exercise 3: Analyze the FLYA results
- 3 Using Talos to generate torsion angle restraints
- 3.1 Exercise 4: Calculate backbone torsion angle restraints using Talos
- 4 Automated NOESY assignment and structure calculation
- 4.1 Exercise 5: Run noeassign
- 4.1.1 The noeassign CALC macro
- 5 Creating the ligand library file for CYANA
- 5.1 Exercise 6: Drawing the molecule and obtaining the SMILES code
- 5.2 Exercise 7: Converting the SMILES code to mol2
- 5.3 Exercise 8: Converting the mol2 file to a lib file for CYANA
- 5.4 Alternative Exercise 6-8: Converting a pdb file to a lib file for CYANA
- 6 Calculating the structure of the protein-ligand complex
- 6.1 Exercise 9: (Semi-automatic) Intermolecular cross peaks assignment and structure calculation
- 7 Comparing the calculated NMR structure to an XRAY reference structure
- 7.1 Exercise 10: Compare the NMR structure to the Xray structure
- 7.2 Exercise 11: Preparing an xray structure to use within CYANA
- 7.3 Exercise 12: Calclulate the RMSD of NMR vs. xray structure using a CYANA macro
- 8 Beyond The Basics: Improving the final structure
- 8.1 FLYA options
- 8.2 neoassign options
- 8.3 Exercise 13: Mapping restraints onto a known structure
- 8.4 Exercise 14: Work on improving the final structure
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CYANA setup
Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):
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