Dear Meisam, For me it does work and if I import a cif dictionary it will override the existing definition. I default use INH for the ligand name which has already been taken by the pdb without any problems.
Assuming that you have used the correct procedure to import the cif directory in refmac and coot, the thing to check is whether your cif directory really matches your pdb file. The most likely error is that the residue name assigned by jligand is different from the name you gave to the ligand in the pdb. The second most likely source of error is that the atom names do not match. You should check with an editor whether both ligand name and atom names match and if necessary, correct them. Good luck! Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Meisam Nosrati Gesendet: Dienstag, 1. April 2014 01:22 An: [email protected] Betreff: [ccp4bb] Refinement with new ligands to PDB 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. Thanks in advance for your help Meisam
