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Task 4: Calculate the structure of the ligand molecule.
- In the task4_to_5 6 directory,
create a text file using a text editor, the ".upl" file (mol.upl).
This name is used in the instruction file for CYANA, the CALC.cya file in this exercise. - To do that, copy the "Intermolecular NOE" table - the first column contains the 6 columns needed for identification of the atom pair.
- The seventh column has to be the distance calculated above.
Note that the atom numbers and names have to exactly match the MOL.lib file.
Note also, that the distance has to be in a numerical format using "dot" as a decimal separator and not a "comma"!
- Navigate to the task4_to_5 6 directory in the terminal (command line) and start the CYANA:
$ cyana - In the cyana prompt, call the instruction in CALC.cya (leaving out the .cya) to perform the structure calculation:
cyana> CALC
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- Copy the calc_ligand_structure into a new one.
cp -r task4_to_56 task4_to_56_noSD - Open the mol.upl In the text editor, delete the line with the problematic restraint(s).
- Repeat the structure calculation in CYANA:
cyana> CALC
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- 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_56).
- One option is to combine these files:
cat final_protein.upl mol.upl intermolecular.upl > complex.upl
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