Daniele eLBOW can generate the CIF links if put LINK records in the input PDB file. Otherwise you can follow the example here. http://phenix-online.org/documentation/refinement.htm#anch281 Please contact me if you have any more trouble. Nigel On 7/8/2008 8:43 AM, Daniele de Sanctis wrote:Dear all, I have a trisaccharide in my structure, and I generate the cif file with elbow (see below). Unfortunately phenix.refine seems not recognizing the bonds C5-O1 between different units and is not keeping the chain together. As far as I could understand I should also use the keyword "apply_cif_link", but I couldn't find which syntax i should use. Thanks for the help Daniele # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.3b (Mon Nov 20 17:20:00 2007) # - file written: Mon Jul 7 18:19:22 2008 # # Input file: a3.pdb # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level AHR AHR 'Unknown ' ligand 15 9 . # data_comp_AHR # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z AHR 'C5'' C CH3 . 61.3311 15.7148 36.7946 AHR 'C4'' C CR5 . 60.1817 16.4682 36.1126 AHR 'O4'' O O . 60.3257 17.5507 35.0934 AHR 'C3'' C CR5 . 58.6911 16.2438 36.3556 AHR 'O3'' O OC . 58.1296 15.2877 37.2130 AHR 'C2'' C CR5 . 57.9427 17.1885 35.4852 AHR 'O2'' O OC . 56.5500 17.3383 35.4371 AHR 'C1'' C CR5 . 58.9640 18.0045 34.6971 AHR 'O1'' O OH1 . 58.6701 18.9985 33.7515 AHR 'H5'1' H HCH3 . 61.2131 14.6537 36.6320 AHR 'H5'2' H HCH3 . 61.3175 15.9201 37.8548 AHR 'H5'3' H HCH3 . 62.2726 16.0401 36.3773 AHR 'H3'1' H H . 57.7021 15.7812 38.0734 AHR 'H2'1' H H . 56.1521 16.7529 34.6214 AHR 'H1'1' H HOH1 . 59.4063 19.7861 33.8153 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd AHR 'C5'' 'C4'' single 1.53429 0.02 AHR 'C4'' 'O4'' aromatic 1.49380 0.02 AHR 'C4'' 'C3'' aromatic 1.52685 0.02 AHR 'O4'' 'C1'' aromatic 1.48900 0.02 AHR 'C3'' 'O3'' double 1.40168 0.02 AHR 'C3'' 'C2'' aromatic 1.48663 0.02 AHR 'C2'' 'O2'' double 1.40154 0.02 AHR 'C2'' 'C1'' aromatic 1.52635 0.02 AHR 'C1'' 'O1'' single 1.40306 0.02 AHR 'H5'1' 'C5'' single 1.08000 0.02 AHR 'H5'2' 'C5'' single 1.08000 0.02 AHR 'H5'3' 'C5'' single 1.08000 0.02 AHR 'H3'1' 'O3'' single 1.08000 0.02 AHR 'H2'1' 'O2'' single 1.08000 0.02 AHR 'H1'1' 'O1'' single 1.08000 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd AHR 'O4'' 'C4'' 'C5'' 125.93952 3.0 AHR 'C3'' 'C4'' 'C5'' 126.05117 3.0 AHR 'H5'1' 'C5'' 'C4'' 109.48717 3.0 AHR 'H5'2' 'C5'' 'C4'' 109.48699 3.0 AHR 'H5'3' 'C5'' 'C4'' 109.47730 3.0 AHR 'C1'' 'O4'' 'C4'' 108.31507 3.0 AHR 'O3'' 'C3'' 'C4'' 126.06060 3.0 AHR 'C2'' 'C3'' 'C4'' 107.75208 3.0 AHR 'C3'' 'C4'' 'O4'' 108.00930 3.0 AHR 'C2'' 'C1'' 'O4'' 108.15545 3.0 AHR 'O1'' 'C1'' 'O4'' 125.92746 3.0 AHR 'H3'1' 'O3'' 'C3'' 109.52327 3.0 AHR 'O2'' 'C2'' 'C3'' 126.02920 3.0 AHR 'C1'' 'C2'' 'C3'' 107.76809 3.0 AHR 'C2'' 'C3'' 'O3'' 126.15656 3.0 AHR 'H2'1' 'O2'' 'C2'' 109.52075 3.0 AHR 'O1'' 'C1'' 'C2'' 125.91301 3.0 AHR 'C1'' 'C2'' 'O2'' 126.15898 3.0 AHR 'H1'1' 'O1'' 'C1'' 109.51700 3.0 AHR 'H5'2' 'C5'' 'H5'1' 109.46605 3.0 AHR 'H5'3' 'C5'' 'H5'1' 109.45474 3.0 AHR 'H5'3' 'C5'' 'H5'2' 109.45508 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period AHR CONST_01 'C2'' 'C1'' 'O4'' 'C4'' 0.00000 0.0 0 AHR CONST_02 'C1'' 'C2'' 'C3'' 'C4'' -0.00000 0.0 0 AHR CONST_03 'C2'' 'C3'' 'C4'' 'O4'' 0.00000 0.0 0 AHR CONST_04 'C3'' 'C2'' 'C1'' 'O4'' -0.00000 0.0 0 AHR CONST_05 'C1'' 'O4'' 'C4'' 'C3'' -0.00000 0.0 0 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd AHR plan-1 'C4'' 0.020 AHR plan-1 'O4'' 0.020 AHR plan-1 'C1'' 0.020 AHR plan-1 'C2'' 0.020 AHR plan-1 'C3'' 0.020 AHR plan-1 'C5'' 0.050 AHR plan-1 'O1'' 0.050 AHR plan-1 'O2'' 0.050 AHR plan-1 'O3'' 0.050 AHR plan-2 'C4'' 0.100 AHR plan-2 'O4'' 0.100 AHR plan-2 'C5'' 0.100 AHR plan-2 'C3'' 0.100 AHR plan-3 'C3'' 0.100 AHR plan-3 'O3'' 0.100 AHR plan-3 'C4'' 0.100 AHR plan-3 'C2'' 0.100 AHR plan-4 'C2'' 0.100 AHR plan-4 'O2'' 0.100 AHR plan-4 'C3'' 0.100 AHR plan-4 'C1'' 0.100