Hi Meisam, I use the elbow module in phenix to generate the cif file which you then need to add in to the refinement module of phenix.refine. Be sure to use the new pdb which is generated.
Once you have generated your ligand you should be able to read the new pdb file and cif file into Coot to check that it works (edit chi angles) In some cases jligand and other cif generators can make errors in new ligands and the cif files can be flawed. It is good to look into these yourself to help better understand them. Try elbow first Hope this helps J -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Meisam Nosrati Sent: Tuesday, 1 April 2014 12:22 p.m. To: [email protected] Subject: [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
