Dear Meisam,
In the past I had similar problems, because of jligand and other cif
generators can make errors when generate cif files, as it has been
written before. I have solved these problems by using sketcher (ccp4)
and PRODRG server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg).
I use the first one to create the pdb file (it is very easy to use) and
the second to generate the restrains file both for refmac and for
phenix.refine.
I hope I've helped you.
Danilo
Il 2014-04-01 01:21 Meisam Nosrati ha scritto:
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
