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Sorry for the duplicate post: My email is [EMAIL PROTECTED] Thanks. ________________________________ CCP4 BB, I have two proteins that form a heterodimer and have generated a chemical crosslink between them. The crosslinking reagent is used to couple carboxyl groups to primary amines. In my case, it has catalyzed the formation of a amide bond between a glutamic acid side chain from one protein a lysine amine side chain of the second. I have 2.4 A data and would like to refine the model. The crosslink is clearly visible in the electron density map. I have tried the following: 1. Created two 'new' amino acids: GXX and LYX, which only differ from the definitions for GLU and LYS in the atoms which are not present because of the crosslink. 2. Created a new link called XLINK (based on the definition of the TRANS link) 3. Put these three files into a single file which I read in when I run refmac (attached below) 4. I have added the 'LINK' to the pdb file as well: LINK GXX A 2 LYX B 401 XLINK I get the following error from refmac. ERR: item _chem_link_bond.link_id :XLINK not found in the list of links BLOCK :data_link_XLINK I've included the library file I created below. It is organized like the mon_lib.cif file and the monomer descriptions are followed by the link descriptions. Why doesn't refmac read in the link? Thanks in advance, Rebecca global_ _lib_name mon_lib_EDIT _lib_version 4.7 _lib_update 05/10/06 # ------------------------------------------------ # # --- LIST OF MONOMERS --- # 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 LYX LYX 'CROSSLINKED-LYSINE ' L-peptide 20 9 . GXX GXX 'CROSSLINKED-GLUTAMATE ' L-peptide 14 8 . # # --- DESCRIPTION OF MONOMERS --- # data_comp_GXX # 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 GXX N N NH1 -0.204 GXX H H HNH1 0.204 GXX CA C CH1 0.058 GXX HA H HCH1 0.046 GXX CB C CH2 -0.078 GXX HB1 H HCH2 0.039 GXX HB2 H HCH2 0.039 GXX CG C CH2 -0.067 GXX HG1 H HCH2 0.041 GXX HG2 H HCH2 0.041 GXX CD C C 0.318 GXX OE1 O OC -0.422 GXX C C C 0.318 GXX O O O -0.422 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type GXX N n/a CA START GXX H N . . GXX CA N C . GXX HA CA . . GXX CB CA CG . GXX HB1 CB . . GXX HB2 CB . . GXX CG CB CD . GXX HG1 CG . . GXX HG2 CG . . GXX OE1 CD . . GXX C CA . END GXX O C . . 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 GXX N H coval 0.860 0.020 GXX N CA coval 1.458 0.019 GXX CA HA coval 0.980 0.020 GXX CA CB coval 1.530 0.020 GXX CB HB1 coval 0.970 0.020 GXX CB HB2 coval 0.970 0.020 GXX CB CG coval 1.520 0.030 GXX CG HG1 coval 0.970 0.020 GXX CG HG2 coval 0.970 0.020 GXX CG CD coval 1.516 0.025 GXX CD OE1 coval 1.249 0.019 GXX CA C coval 1.525 0.021 GXX C O coval 1.231 0.020 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 GXX H N CA 114.000 3.000 GXX HA CA CB 109.000 3.000 GXX CB CA C 110.100 1.900 GXX HA CA C 109.000 3.000 GXX N CA HA 110.000 3.000 GXX N CA CB 110.500 1.700 GXX HB1 CB HB2 110.000 3.000 GXX HB2 CB CG 108.000 3.000 GXX HB1 CB CG 108.000 3.000 GXX CA CB HB1 109.000 3.000 GXX CA CB HB2 109.000 3.000 GXX CA CB CG 114.100 2.000 GXX HG1 CG HG2 110.000 3.000 GXX HG2 CG CD 108.000 3.000 GXX HG1 CG CD 108.000 3.000 GXX CB CG HG1 109.000 3.000 GXX CB CG HG2 109.000 3.000 GXX CB CG CD 112.600 1.700 GXX CG CD OE1 118.400 2.300 GXX N CA C 111.200 2.800 GXX CA C O 120.800 1.700 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 GXX chi1 N CA CB CG 180.000 15.000 3 GXX chi2 CA CB CG CD 180.000 15.000 3 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign GXX chir_01 CA N CB C negativ 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 GXX plan CD 0.020 GXX plan CG 0.020 GXX plan OE1 0.020 # ------------------------------------------------------ LYX LYX 'LYXINE ' L-peptide 22 9 . # data_comp_LYX # 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 LYX N N NH1 -0.204 LYX H H HNH1 0.204 LYX CA C CH1 0.058 LYX HA H HCH1 0.046 LYX CB C CH2 -0.076 LYX HB1 H HCH2 0.038 LYX HB2 H HCH2 0.038 LYX CG C CH2 -0.076 LYX HG1 H HCH2 0.038 LYX HG2 H HCH2 0.038 LYX CD C CH2 -0.076 LYX HD1 H HCH2 0.038 LYX HD2 H HCH2 0.038 LYX CE C CH2 -0.013 LYX HE1 H HCH2 0.098 LYX HE2 H HCH2 0.098 LYX NZ N NT3 -0.204 LYX HZ1 H HNT3 0.204 LYX C C C 0.318 LYX O O O -0.422 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type LYX N n/a CA START LYX H N . . LYX CA N C . LYX HA CA . . LYX CB CA CG . LYX HB1 CB . . LYX HB2 CB . . LYX CG CB CD . LYX HG1 CG . . LYX HG2 CG . . LYX CD CG CE . LYX HD1 CD . . LYX HD2 CD . . LYX CE CD NZ . LYX HE1 CE . . LYX HE2 CE . . LYX NZ CE HZ3 . LYX HZ1 NZ . . LYX C CA . END LYX O C . . 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 LYX N H coval 0.860 0.020 LYX N CA coval 1.458 0.019 LYX CA HA coval 0.980 0.020 LYX CA CB coval 1.530 0.020 LYX CB HB1 coval 0.970 0.020 LYX CB HB2 coval 0.970 0.020 LYX CB CG coval 1.520 0.030 LYX CG HG1 coval 0.970 0.020 LYX CG HG2 coval 0.970 0.020 LYX CG CD coval 1.520 0.030 LYX CD HD1 coval 0.970 0.020 LYX CD HD2 coval 0.970 0.020 LYX CD CE coval 1.520 0.030 LYX CE HE1 coval 0.970 0.020 LYX CE HE2 coval 0.970 0.020 LYX CE NZ coval 1.489 0.030 LYX NZ HZ1 coval 0.960 0.020 LYX CA C coval 1.525 0.021 LYX C O coval 1.231 0.020 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 LYX H N CA 114.000 3.000 LYX HA CA CB 109.000 3.000 LYX CB CA C 110.100 1.900 LYX HA CA C 109.000 3.000 LYX N CA HA 110.000 3.000 LYX N CA CB 110.500 1.700 LYX HB1 CB HB2 110.000 3.000 LYX HB2 CB CG 108.000 3.000 LYX HB1 CB CG 108.000 3.000 LYX CA CB HB1 109.000 3.000 LYX CA CB HB2 109.000 3.000 LYX CA CB CG 114.100 2.000 LYX HG1 CG HG2 110.000 3.000 LYX HG2 CG CD 108.000 3.000 LYX HG1 CG CD 108.000 3.000 LYX CB CG HG1 109.000 3.000 LYX CB CG HG2 109.000 3.000 LYX CB CG CD 111.300 2.300 LYX HD1 CD HD2 110.000 3.000 LYX HD2 CD CE 108.000 3.000 LYX HD1 CD CE 108.000 3.000 LYX CG CD HD1 109.000 3.000 LYX CG CD HD2 109.000 3.000 LYX CG CD CE 111.300 2.300 LYX HE1 CE HE2 110.000 3.000 LYX HE2 CE NZ 108.000 3.000 LYX HE1 CE NZ 108.000 3.000 LYX CD CE HE1 109.000 3.000 LYX CD CE HE2 109.000 3.000 LYX CD CE NZ 111.900 3.200 LYX CE NZ HZ1 110.000 3.000 LYX N CA C 111.200 2.800 LYX CA C O 120.800 1.700 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 LYX chi1 N CA CB CG 180.000 15.000 3 LYX chi2 CA CB CG CD 180.000 15.000 3 LYX chi3 CB CG CD CE 180.000 15.000 3 LYX chi4 CG CD CE NZ 180.000 15.000 3 LYX hh CD CE NZ HZ1 60.000 30.000 3 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign LYX chir_01 CA N CB C negativ # ------------------------------------------------------ # --- LIST OF LINKS --- # data_link_list loop_ _chem_link.id _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 _chem_link.name XLINK GXX . . LYX . . AMIDE-XLINK data_link_XLINK # 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 XLINK 1 CD 2 NZ single 1.329 0.014 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 XLINK 1 OE1 1 CD 2 NZ 123.000 1.600 XLINK 1 CG 1 CD 2 NZ 116.200 2.000 XLINK 1 CD 2 NZ 2 HZ1 124.300 3.000 XLINK 1 CD 2 NZ 2 CE 121.700 1.800 loop_ _chem_link_tor.link_id _chem_link_tor.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 XLINK psi 1 CB 1 CG 1 CD 2 NZ 160.00 30.0 2 XLINK omega 1 CG 1 CD 2 NZ 2 CE 180.00 5.0 0 XLINK phi 1 CD 2 NA 2 CE 2 CD 60.00 20.0 3 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 XLINK plane1 1 CG 0.020 XLINK plane1 1 CD 0.020 XLINK plane1 1 OE1 0.020 XLINK plane1 2 NZ 0.020 XLINK plane2 1 CD 0.020 XLINK plane2 2 NZ 0.020 XLINK plane2 2 CE 0.020 XLINK plane2 2 HZ1 0.020 #
