...
Look at the structures using chimera molecular viewer.
Part 3
Task 1: Calculate the structure of the protein-ligand complex.
- Prepare the intermolecular distance restraints. For that, follow the same steps as in
Part1, Task 3, but for the Table: "Intermolecular NOE". Use the same same pair of atoms for calibration of the distances. - In the part3 directory, place the the distances into intermolecular.upl
- Copy the also the mol.upl file here from the Part1, Task 4 (part1/task4_to_5).
- One option is to combine these files:
cat final_protein.upl mol.upl intermolecular.upl > complex.upl
...
- 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 how robust the calculation of the protein-ligand structure is.
Task 2: Redo the normalization
NMR2
NMR2 runs via the platform SAMSON.
...