Seitenhistorie

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1. Open the overview file in the text editor or a text viewer (less demo.ovw).
   Find the statement "Restraints violated" and identify into which atoms it belong.
2. Look at structure using chimera.
   1. for clarity, select only the first structure:
      select -> chain -> A demo.pdb #0.1
      select -> Invert (all models)
      actions -> Atoms/Bonds -> delete 
3. in the molecular viewer.
   Explain the violation.
   Is such a problem more likely for atoms short or long apart?
4. Plot normalized BUbuildup curves
   Calculate normalized NOESY buildup curves, by dividing them by the diagonal peaks (for now, use the first table of the
   diagonal peaks). Plot the buildup curves and comment on their shape. Can you explain the changed shapes?
   Can you see the case(s) with spin diffusion more clearly?

Task 6: Remove spin diffusion and repeat the calculation

1. Copy the calc_ligand_structure into a new one.
   cp -r

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1. task_4_to_5 task_4_to_5_noSD 
2. Open the mol.upl In the text editor, delete the line with the  problematic restrain.
3. Repeat the structure calculation in CYANA:
   cyana> reg

Compare the structures 

Task 7 (optional)

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In this short exercise, we will calculate the protein structure using ready distances stored in the final_protein.upl
file. We do not need any extra library file, as this time, the sequence file (demoShort.seq) contains only standard
aminoacid residues.

• In the

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• part2 directory, execute
  cyana reg.cya

Look at the structures using chimera molecular viewer.

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1. Prepare the intermolecular distance restraints. For that, follow the same steps as in
   Task 3, but for the Table: "Intermolecular Intermolecular NOE". Use the same same pair of atoms for calibration of the distances.
2. In the calc_protein_ligand_complex_structure part3 directory
   place the the distances into
   intermolecular.upl
3. Copy the also the  mol mol.upl file here from the Task 4 (part1/task4_to_5).
4. One option is to combine these files:

   cat final_protein.upl mol.upl intermolecular.upl > complex.upl

• calculate the structure:
  cyana reg.cya
  check the resulting structure using chimera
• for clarity, select only the first structure :
  select -> chain -> A demo.pdb #0.1
  select -> Invert (all models)
  actions -> Atoms/Bonds -> delete(as in Task 5)
  
  

Note! if using VMD as a molecular viewer, it will refuse to recognize large parts of the secondary structure!
Try to explain what can be causing it.
Check the median of the distance restraints placed into .upl
It should be around 4.2 for intramolecular distances, and 4.4 for the intermolecular distances.
What do you get? discuss.

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