Hi Andrea You need to have an appropriate LINK record in the PDB file but you also need to specify the link restraints in the CIF file, for example:
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 B01 HIS 'HISTIDINE' L-peptide 18 10 . L01 . 'boronate-4-L01' non-polymer 29 17 . data_link_list loop_ _chem_link.id _chem_link.name _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 N01 N01 B01 . . L01 . . data_link_N01 loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd N01 1 NE2 2 B2 single 1.511 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd N01 2 O1 2 B2 1 NE2 109.1 3.0 N01 1 NE2 2 B2 2 O3 109.0 3.0 N01 1 NE2 2 B2 2 C18 109.4 3.0 N01 2 B2 1 NE2 1 CD2 126.4 2.1 N01 2 B2 1 NE2 1 CE1 126.6 2.1 loop_ _chem_link_tor.link_id _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_id_1 _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_id_2 _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_id_3 _chem_link_tor.atom_4_comp_id _chem_link_tor.atom_id_4 _chem_link_tor.value_angle _chem_link_tor.value_angle_esd _chem_link_tor.period N01 2 CB 2 O1 2 B2 1 NE2 60 30.00 3 N01 2 O1 2 B2 1 NE2 1 CD2 30 30.00 6 loop_ _chem_link_chir.link_id _chem_link_chir.atom_1_comp_id _chem_link_chir.atom_id_1 _chem_link_chir.atom_2_comp_id _chem_link_chir.atom_id_2 _chem_link_chir.atom_3_comp_id _chem_link_chir.atom_id_3 _chem_link_chir.atom_4_comp_id _chem_link_chir.atom_id_4 _chem_link_chir.volume_sign N01 2 B2 2 O1 1 NE2 2 O3 negativ loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd N01 plan_01 2 B2 0.010 N01 plan_01 1 NE2 0.010 N01 plan_01 1 CD2 0.010 N01 plan_01 1 CG 0.010 N01 plan_01 1 CB 0.010 N01 plan_01 1 ND1 0.010 N01 plan_01 1 HD1 0.010 N01 plan_01 1 CE1 0.010 N01 plan_01 1 HD2 0.010 N01 plan_01 1 HE1 0.010 In this case it was a boronate compound covalently bound to a HIS s/c with the B atom in the plane. Hope this helps! -- Ian On 28 November 2012 07:03, Andrea Pica <[email protected]> wrote: > Hi everybody! > > Is there a simple way in REFMAC to restraints a group of atoms belonging > to different residues to lay on a plane? Of course I would like to set the > sigma! > > Do I have to add any line in the PDB header? Is it that simple? > > Thank you very much! > > Andrea > > > Andrea Pica, Ph.D. student > University of Naples "Federico II" > Department of Chemical Sciences - Room 1N-04 > Complesso Universitario Monte S. Angelo > Via Cintia > I-80126 Naples - Italy > Phone 39-081 674269 > Fax 39-081 674090 >
