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We will use a ready .lib file in our exercise.
We complete the information by a .seq file with a "sequence" containing only one line the name and number of the residue (MOL 999)
The other information: the distance restraints are obtained by CYANA from a separate text file, where
the pairs of atoms are identified by three and three columns, and the distance in Ånsgrom.
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Task 4: Calculate the structure of the ligand molecule.
- In the task_4_to_5 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 reg.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 calctask_4_ligandto_structure 5 directory in the terminal (command line) and start the CYANA:
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