Dear Chris, this did it for me. Create a file which you can call whatever you want even the extension doesn't matter. E.g.: cif_link.params Put in this file your links: (Which Atom of residue1 will be connected to which Atom in residue2 is already defined in mon_lib_list.cif) refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname ASN and resid 297 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname NAG and resid 501 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 501 residue_selection_2 = chain A and resname BMA and resid 502 } refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-3. residue_selection_1 = chain A and resname BMA and resid 502 residue_selection_2 = chain A and resname MAN and resid 503 } 4) add this file in the GUI Or run % phenix.refine model.pdb data.hkl cif_link.params 5)Trouble shooting a)run iotbx.phil cif_link.params (this checks if the syntax is right) b) check .eff file the links should be added there. You can also check the . geo file if you see anything strange. c)Having unknown to phenix.refine item in PDB file (novel ligand, etc... (BMA is also not there) ). phenix.refine uses the CCP4 Monomer Library as the source of stereochemical information for building geometry restraints and reporting statistics. If phenix.refine is unable to match an item in input PDB file against the Monomer Library it will stop with "Sorry" message explaining what to do and listing the problem atoms. If this happened, it is necessary to obtain a cif file (parameter file, describing unknown molecule) by either making it manually or having eLBOW program to generate it: phenix.elbow model.pdb --do-all --output=all_ligands this will ask eLBOW to inspect the model_new.pdb file, find all unknown items in it and create one cif file for them all_ligands.cif. Alternatively, one can specify a three-letters name for the unknown residue: phenix.elbow model.pdb --residue=MAN --output=man !Check the file if everything is ok! Please correct if this is not ok, or there is an easier way now. Kind regards George. -----Ursprüngliche Nachricht----- Von: [email protected] [mailto:[email protected]] Im Auftrag von Chris Ulens Gesendet: Monday, May 31, 2010 9:14 PM An: PHENIX user mailing list Betreff: Re: [phenixbb] NAG-NAG description Dear glycobiologists and phenixfriends. I am trying to refine a NAG-NAG chain attached to an Asn122 in my (pentameric) structure. What is the proper description in the cif_link.params that is the equivalent of the pdb description pasted below that phenix so kindly ignores? Also, what is the proper way to define the cif_link.params file in the GUI? Thank you. -Chris LINK ND2 ASN A 122 C1 NAG A 834 1555 1555 1.37 LINK O4 NAG A 834 C1 NAG A 835 1555 1555 1.43 LINK ND2 ASN B 122 C1 NAG B 834 1555 1555 1.37 LINK O4 NAG B 834 C1 NAG B 835 1555 1555 1.43 LINK ND2 ASN C 122 C1 NAG C 834 1555 1555 1.37 LINK O4 NAG C 834 C1 NAG C 835 1555 1555 1.43 LINK ND2 ASN D 122 C1 NAG D 834 1555 1555 1.37 LINK O4 NAG D 834 C1 NAG D 835 1555 1555 1.43 LINK ND2 ASN E 122 C1 NAG E 834 1555 1555 1.37 LINK O4 NAG E 834 C1 NAG E 835 1555 1555 1.43 --------------------------------------------------- Chris Ulens, Ph.D. Lab of Structural Neurobiology Department of Molecular Cell Biology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium e [email protected] t +32 16 345812 f +32 16 345699 w http://www.xtal.be _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb