On 01/04/14 00:21, Meisam Nosrati wrote:
Dear CCP4ers
I have crystallized a protein with a series of ligands that are not in the PDB.
I have made the pdb and the torsion libraries in the jligand and given them the
new three letter codes, and then I try the refinement in the PHENIX or CCP4,
but since these ligands are not in the library the refinement aborts. Even when
I open the ligand files in COOT and I import the cif dictionary, still it does
not recognize it, and does not let me rotate around the bonds.
I need to know how to fix this problem, and how can I choose the three letter
codes for my ligands that are not already chosen by other people.
What does coot say in the terminal when you try to read in the cif file?
The Chemical Component Dictionary tells you which three-letter-codes
have been assigned.
http://www.wwpdb.org/ccd.html
P.
