Dear CCP4s, Apologize if this was answered before.
We are using the latest version of CCP4 and have a problem running sketcher. When creating the library description from a displayed structure we are getting an error when using the option regularise the structure with Refmac. The program creates the pdb and the corresponding cif file but while we can read the pdb with coot the cif file is unreadable (no restrains found error). Looking into details at the files we realised that atoms are incorrectly written in the pdb (i.e. shifted). Any idea how to solve the problem, a part from writing a script that will put the atoms back to their corresponding position and of course not using the regularise option.
Best regards, IrenaPS. I am sending attached an example of pdb/cifs created with/without the regularise option
-- Irena Bonin PhD Head of Structural Biology CrystaX Pharmaceuticals S.L. Barcelona Science Park Baldiri Reixac 10-12 08028 Barcelona, Spain Tel: +34 93 112 20 742 Fax: +34 93 377 40 28 email: [email protected] www.crystax.com The information contained in this message is proprietary and confidential and is only and exclusively addressed to designated recipient(s). If you are not the intended recipient, you are hereby notified that any unauthorized use, distribution and/or copying is prohibited by virtue of the legislation in force. If you have received this e-mail in error, please notify us immediately by e-mail and delete it completely from all computers -- Irena Bonin PhD Head of Structural Biology CrystaX Pharmaceuticals S.L. Barcelona Science Park Baldiri Reixac 10-12 08028 Barcelona, Spain Tel: +34 93 112 20 742 Fax: +34 93 377 40 28 email: [email protected] www.crystax.com The information contained in this message is proprietary and confidential and is only and exclusively addressed to designated recipient(s). If you are not the intended recipient, you are hereby notified that any unauthorized use, distribution and/or copying is prohibited by virtue of the legislation in force. If you have received this e-mail in error, please notify us immediately by e-mail and delete it completely from all computers -- Irena Bonin PhD Head of Structural Biology CrystaX Pharmaceuticals S.L. Barcelona Science Park Baldiri Reixac 10-12 08028 Barcelona, Spain Tel: +34 93 112 20 742 Fax: +34 93 377 40 28 email: [email protected] www.crystax.com The information contained in this message is proprietary and confidential and is only and exclusively addressed to designated recipient(s). If you are not the intended recipient, you are hereby notified that any unauthorized use, distribution and/or copying is prohibited by virtue of the legislation in force. If you have received this e-mail in error, please notify us immediately by e-mail and delete it completely from all computers
TEST_libcheck_non regularised.pdb
Description: Protein Databank data
global_ _lib_name ? _lib_version ? _lib_update ? # ------------------------------------------------ # # --- 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 TEST TES '1 ' non-polymer 27 15 . # # --- DESCRIPTION OF MONOMERS --- # data_comp_TEST # 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 TEST O1 O OH1 0.000 0.000 0.000 0.000 TEST HO1 H H 0.000 0.255 -0.920 -0.155 TEST C7 C CR6 0.000 1.121 0.783 0.060 TEST C8 C CR16 0.000 0.875 2.161 0.173 TEST H4 H H 0.000 -0.149 2.515 0.164 TEST C9 C CR16 0.000 1.908 3.083 0.296 TEST H5 H H 0.000 1.719 4.149 0.267 TEST C10 C CR16 0.000 3.182 2.584 0.455 TEST H6 H H 0.000 4.021 3.262 0.541 TEST C11 C CR16 0.000 3.393 1.204 0.505 TEST H1 H H 0.000 4.407 0.841 0.613 TEST C6 C CR6 0.000 2.356 0.270 0.421 TEST C5 C CR5 0.000 2.676 -1.187 0.441 TEST O2 O O2 0.000 2.932 -2.003 -0.621 TEST C3 C CR15 0.000 3.274 -3.290 -0.246 TEST H3 H H 0.000 3.593 -4.101 -0.888 TEST C4 C CR15 0.000 2.846 -2.004 1.528 TEST H9 H H 0.000 2.778 -1.682 2.560 TEST C2 C CR5 0.000 3.121 -3.313 1.115 TEST C1 C CH2 0.000 3.323 -4.345 2.196 TEST H11 H H 0.000 2.742 -4.044 3.070 TEST H12 H H 0.000 4.384 -4.367 2.455 TEST C12 C C1 0.000 2.895 -5.687 1.757 TEST H__1 H H 0.000 1.858 -5.960 1.856 TEST C13 C C2 0.000 3.736 -6.561 1.249 TEST H132 H H 0.000 4.776 -6.305 1.143 TEST H131 H H 0.000 3.382 -7.529 0.942 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 TEST O1 n/a C7 START TEST HO1 O1 . . TEST C7 O1 C8 . TEST C8 C7 C9 . TEST H4 C8 . . TEST C9 C8 C10 . TEST H5 C9 . . TEST C10 C9 C11 . TEST H6 C10 . . TEST C11 C10 C6 . TEST H1 C11 . . TEST C6 C11 C5 . TEST C5 C6 C4 . TEST O2 C5 C3 . TEST C3 O2 H3 . TEST H3 C3 . . TEST C4 C5 C2 . TEST H9 C4 . . TEST C2 C4 C1 . TEST C1 C2 C12 . TEST H11 C1 . . TEST H12 C1 . . TEST C12 C1 C13 . TEST H__1 C12 . . TEST C13 C12 H131 . TEST H132 C13 . . TEST H131 C13 . END TEST C2 C3 . ADD TEST C6 C7 . ADD 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 TEST C1 C2 single 1.510 0.020 TEST C2 C3 double 1.387 0.020 TEST C2 C4 single 1.387 0.020 TEST C3 O2 single 1.380 0.020 TEST O2 C5 single 1.370 0.020 TEST H9 C4 single 1.083 0.020 TEST C4 C5 double 1.387 0.020 TEST C5 C6 single 1.490 0.020 TEST C6 C7 aromatic 1.384 0.020 TEST C6 C11 aromatic 1.390 0.020 TEST C7 O1 single 1.362 0.020 TEST C8 C7 aromatic 1.390 0.020 TEST HO1 O1 single 0.967 0.020 TEST H4 C8 single 1.083 0.020 TEST C9 C8 aromatic 1.390 0.020 TEST H5 C9 single 1.083 0.020 TEST C10 C9 aromatic 1.390 0.020 TEST H6 C10 single 1.083 0.020 TEST C11 C10 aromatic 1.390 0.020 TEST H1 C11 single 1.083 0.020 TEST C12 C1 single 1.510 0.020 TEST C13 C12 double 1.320 0.020 TEST H11 C1 single 1.092 0.020 TEST H12 C1 single 1.092 0.020 TEST H3 C3 single 1.083 0.020 TEST H__1 C12 single 1.077 0.020 TEST H131 C13 single 1.077 0.020 TEST H132 C13 single 1.077 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 TEST HO1 O1 C7 109.470 3.000 TEST O1 C7 C8 120.000 3.000 TEST O1 C7 C6 120.000 3.000 TEST C8 C7 C6 120.000 3.000 TEST C7 C8 H4 120.000 3.000 TEST C7 C8 C9 120.000 3.000 TEST H4 C8 C9 120.000 3.000 TEST C8 C9 H5 120.000 3.000 TEST C8 C9 C10 120.000 3.000 TEST H5 C9 C10 120.000 3.000 TEST C9 C10 H6 120.000 3.000 TEST C9 C10 C11 120.000 3.000 TEST H6 C10 C11 120.000 3.000 TEST C10 C11 H1 120.000 3.000 TEST C10 C11 C6 120.000 3.000 TEST H1 C11 C6 120.000 3.000 TEST C11 C6 C5 120.000 3.000 TEST C11 C6 C7 120.000 3.000 TEST C5 C6 C7 120.000 3.000 TEST C6 C5 O2 126.000 3.000 TEST C6 C5 C4 126.000 3.000 TEST O2 C5 C4 108.000 3.000 TEST C5 O2 C3 108.000 3.000 TEST O2 C3 H3 126.000 3.000 TEST O2 C3 C2 108.000 3.000 TEST H3 C3 C2 126.000 3.000 TEST C5 C4 H9 126.000 3.000 TEST C5 C4 C2 108.000 3.000 TEST H9 C4 C2 126.000 3.000 TEST C4 C2 C1 126.000 3.000 TEST C4 C2 C3 108.000 3.000 TEST C1 C2 C3 126.000 3.000 TEST C2 C1 H11 109.470 3.000 TEST C2 C1 H12 109.470 3.000 TEST C2 C1 C12 109.500 3.000 TEST H11 C1 H12 107.900 3.000 TEST H11 C1 C12 109.470 3.000 TEST H12 C1 C12 109.470 3.000 TEST C1 C12 H__1 120.000 3.000 TEST C1 C12 C13 120.000 3.000 TEST H__1 C12 C13 120.000 3.000 TEST C12 C13 H132 120.000 3.000 TEST C12 C13 H131 120.000 3.000 TEST H132 C13 H131 120.000 3.000 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 TEST var_1 HO1 O1 C7 C8 175.000 20.000 1 TEST CONST_1 O1 C7 C8 C9 180.000 0.000 0 TEST CONST_2 C7 C8 C9 C10 0.000 0.000 0 TEST CONST_3 C8 C9 C10 C11 0.000 0.000 0 TEST CONST_4 C9 C10 C11 C6 0.000 0.000 0 TEST CONST_5 C10 C11 C6 C5 180.000 0.000 0 TEST CONST_6 C11 C6 C7 O1 180.000 0.000 0 TEST var_2 C11 C6 C5 C4 175.000 20.000 1 TEST CONST_7 C6 C5 O2 C3 180.000 0.000 0 TEST CONST_8 C5 O2 C3 C2 0.000 0.000 0 TEST CONST_9 C6 C5 C4 C2 180.000 0.000 0 TEST CONST_10 C5 C4 C2 C1 180.000 0.000 0 TEST CONST_11 C4 C2 C3 O2 0.000 0.000 0 TEST var_3 C4 C2 C1 C12 175.000 20.000 2 TEST var_4 C2 C1 C12 C13 175.000 20.000 1 TEST CONST_12 C1 C12 C13 H131 180.000 0.000 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 TEST plan-1 C2 0.020 TEST plan-1 C1 0.020 TEST plan-1 C3 0.020 TEST plan-1 C4 0.020 TEST plan-1 O2 0.020 TEST plan-1 C5 0.020 TEST plan-1 H3 0.020 TEST plan-1 H9 0.020 TEST plan-1 C6 0.020 TEST plan-2 C6 0.020 TEST plan-2 C5 0.020 TEST plan-2 C7 0.020 TEST plan-2 C11 0.020 TEST plan-2 C8 0.020 TEST plan-2 C9 0.020 TEST plan-2 C10 0.020 TEST plan-2 O1 0.020 TEST plan-2 H4 0.020 TEST plan-2 H5 0.020 TEST plan-2 H6 0.020 TEST plan-2 H1 0.020 TEST plan-3 C12 0.020 TEST plan-3 C1 0.020 TEST plan-3 C13 0.020 TEST plan-3 H__1 0.020 TEST plan-3 H131 0.020 TEST plan-3 H132 0.020 # ------------------------------------------------------ # ------------------------------------------------------ # ------------------------------------------------------
global_ _lib_name ? _lib_version ? _lib_update ? # ------------------------------------------------ # # --- 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 TEST1 TES '1 ' non-polymer 27 15 . # # --- DESCRIPTION OF MONOMERS --- # data_comp_TEST1 # 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 TEST1 O1 O OH1 0.000 0.000 0.000 0.000 TEST1 HO1 H H 0.000 0.414 -0.870 -0.080 TEST1 C7 C CR6 0.000 0.963 0.963 0.000 TEST1 C8 C CR16 0.000 0.603 2.306 0.000 TEST1 H4 H H 0.000 -0.443 2.586 0.001 TEST1 C9 C CR16 0.000 1.586 3.289 0.000 TEST1 H5 H H 0.000 1.306 4.335 0.001 TEST1 C10 C CR16 0.000 2.929 2.929 0.000 TEST1 H6 H H 0.000 3.695 3.695 0.000 TEST1 C11 C CR16 0.000 3.289 1.586 0.000 TEST1 H1 H H 0.000 4.335 1.306 -0.001 TEST1 C6 C CR6 0.000 2.306 0.603 0.000 TEST1 C5 C CR5 0.000 2.691 -0.836 -0.001 TEST1 O2 O O2 0.000 3.966 -1.328 -0.098 TEST1 C3 C CR15 0.000 3.896 -2.705 -0.061 TEST1 H3 H H 0.000 4.739 -3.382 -0.117 TEST1 C4 C CR15 0.000 1.823 -1.913 0.097 TEST1 H9 H H 0.000 0.745 -1.855 0.187 TEST1 C2 C CR5 0.000 2.576 -3.076 0.059 TEST1 C1 C CH2 0.000 2.039 -4.485 0.136 TEST1 H11 H H 0.000 1.287 -4.630 -0.643 TEST1 H12 H H 0.000 1.582 -4.646 1.115 TEST1 C12 C C1 0.000 3.168 -5.468 -0.062 TEST1 H__1 H H 0.000 4.155 -5.111 -0.306 TEST1 C13 C C2 0.000 2.946 -6.763 0.064 TEST1 H132 H H 0.000 1.960 -7.119 0.309 TEST1 H131 H H 0.000 3.752 -7.463 -0.077 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 TEST1 O1 n/a C7 START TEST1 HO1 O1 . . TEST1 C7 O1 C8 . TEST1 C8 C7 C9 . TEST1 H4 C8 . . TEST1 C9 C8 C10 . TEST1 H5 C9 . . TEST1 C10 C9 C11 . TEST1 H6 C10 . . TEST1 C11 C10 C6 . TEST1 H1 C11 . . TEST1 C6 C11 C5 . TEST1 C5 C6 C4 . TEST1 O2 C5 C3 . TEST1 C3 O2 H3 . TEST1 H3 C3 . . TEST1 C4 C5 C2 . TEST1 H9 C4 . . TEST1 C2 C4 C1 . TEST1 C1 C2 C12 . TEST1 H11 C1 . . TEST1 H12 C1 . . TEST1 C12 C1 C13 . TEST1 H__1 C12 . . TEST1 C13 C12 H131 . TEST1 H132 C13 . . TEST1 H131 C13 . END TEST1 C2 C3 . ADD TEST1 C6 C7 . ADD 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 TEST1 C1 C2 single 1.510 0.020 TEST1 C2 C3 double 1.387 0.020 TEST1 C2 C4 single 1.387 0.020 TEST1 C3 O2 single 1.380 0.020 TEST1 O2 C5 single 1.370 0.020 TEST1 H9 C4 single 1.083 0.020 TEST1 C4 C5 double 1.387 0.020 TEST1 C5 C6 single 1.490 0.020 TEST1 C6 C7 aromatic 1.384 0.020 TEST1 C6 C11 aromatic 1.390 0.020 TEST1 C7 O1 single 1.362 0.020 TEST1 C8 C7 aromatic 1.390 0.020 TEST1 HO1 O1 single 0.967 0.020 TEST1 H4 C8 single 1.083 0.020 TEST1 C9 C8 aromatic 1.390 0.020 TEST1 H5 C9 single 1.083 0.020 TEST1 C10 C9 aromatic 1.390 0.020 TEST1 H6 C10 single 1.083 0.020 TEST1 C11 C10 aromatic 1.390 0.020 TEST1 H1 C11 single 1.083 0.020 TEST1 C12 C1 single 1.510 0.020 TEST1 C13 C12 double 1.320 0.020 TEST1 H11 C1 single 1.092 0.020 TEST1 H12 C1 single 1.092 0.020 TEST1 H3 C3 single 1.083 0.020 TEST1 H__1 C12 single 1.077 0.020 TEST1 H131 C13 single 1.077 0.020 TEST1 H132 C13 single 1.077 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 TEST1 HO1 O1 C7 109.470 3.000 TEST1 O1 C7 C8 120.000 3.000 TEST1 O1 C7 C6 120.000 3.000 TEST1 C8 C7 C6 120.000 3.000 TEST1 C7 C8 H4 120.000 3.000 TEST1 C7 C8 C9 120.000 3.000 TEST1 H4 C8 C9 120.000 3.000 TEST1 C8 C9 H5 120.000 3.000 TEST1 C8 C9 C10 120.000 3.000 TEST1 H5 C9 C10 120.000 3.000 TEST1 C9 C10 H6 120.000 3.000 TEST1 C9 C10 C11 120.000 3.000 TEST1 H6 C10 C11 120.000 3.000 TEST1 C10 C11 H1 120.000 3.000 TEST1 C10 C11 C6 120.000 3.000 TEST1 H1 C11 C6 120.000 3.000 TEST1 C11 C6 C5 120.000 3.000 TEST1 C11 C6 C7 120.000 3.000 TEST1 C5 C6 C7 120.000 3.000 TEST1 C6 C5 O2 126.000 3.000 TEST1 C6 C5 C4 126.000 3.000 TEST1 O2 C5 C4 108.000 3.000 TEST1 C5 O2 C3 108.000 3.000 TEST1 O2 C3 H3 126.000 3.000 TEST1 O2 C3 C2 108.000 3.000 TEST1 H3 C3 C2 126.000 3.000 TEST1 C5 C4 H9 126.000 3.000 TEST1 C5 C4 C2 108.000 3.000 TEST1 H9 C4 C2 126.000 3.000 TEST1 C4 C2 C1 126.000 3.000 TEST1 C4 C2 C3 108.000 3.000 TEST1 C1 C2 C3 126.000 3.000 TEST1 C2 C1 H11 109.470 3.000 TEST1 C2 C1 H12 109.470 3.000 TEST1 C2 C1 C12 109.500 3.000 TEST1 H11 C1 H12 107.900 3.000 TEST1 H11 C1 C12 109.470 3.000 TEST1 H12 C1 C12 109.470 3.000 TEST1 C1 C12 H__1 120.000 3.000 TEST1 C1 C12 C13 120.000 3.000 TEST1 H__1 C12 C13 120.000 3.000 TEST1 C12 C13 H132 120.000 3.000 TEST1 C12 C13 H131 120.000 3.000 TEST1 H132 C13 H131 120.000 3.000 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 TEST1 var_1 HO1 O1 C7 C8 175.000 20.000 1 TEST1 CONST_1 O1 C7 C8 C9 180.000 0.000 0 TEST1 CONST_2 C7 C8 C9 C10 0.000 0.000 0 TEST1 CONST_3 C8 C9 C10 C11 0.000 0.000 0 TEST1 CONST_4 C9 C10 C11 C6 0.000 0.000 0 TEST1 CONST_5 C10 C11 C6 C5 180.000 0.000 0 TEST1 CONST_6 C11 C6 C7 O1 180.000 0.000 0 TEST1 var_2 C11 C6 C5 C4 175.000 20.000 1 TEST1 CONST_7 C6 C5 O2 C3 180.000 0.000 0 TEST1 CONST_8 C5 O2 C3 C2 0.000 0.000 0 TEST1 CONST_9 C6 C5 C4 C2 180.000 0.000 0 TEST1 CONST_10 C5 C4 C2 C1 180.000 0.000 0 TEST1 CONST_11 C4 C2 C3 O2 0.000 0.000 0 TEST1 var_3 C4 C2 C1 C12 175.000 20.000 2 TEST1 var_4 C2 C1 C12 C13 175.000 20.000 1 TEST1 CONST_12 C1 C12 C13 H131 180.000 0.000 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 TEST1 plan-1 C2 0.020 TEST1 plan-1 C1 0.020 TEST1 plan-1 C3 0.020 TEST1 plan-1 C4 0.020 TEST1 plan-1 O2 0.020 TEST1 plan-1 C5 0.020 TEST1 plan-1 H3 0.020 TEST1 plan-1 H9 0.020 TEST1 plan-1 C6 0.020 TEST1 plan-2 C6 0.020 TEST1 plan-2 C5 0.020 TEST1 plan-2 C7 0.020 TEST1 plan-2 C11 0.020 TEST1 plan-2 C8 0.020 TEST1 plan-2 C9 0.020 TEST1 plan-2 C10 0.020 TEST1 plan-2 O1 0.020 TEST1 plan-2 H4 0.020 TEST1 plan-2 H5 0.020 TEST1 plan-2 H6 0.020 TEST1 plan-2 H1 0.020 TEST1 plan-3 C12 0.020 TEST1 plan-3 C1 0.020 TEST1 plan-3 C13 0.020 TEST1 plan-3 H__1 0.020 TEST1 plan-3 H131 0.020 TEST1 plan-3 H132 0.020 # ------------------------------------------------------ # ------------------------------------------------------ # ------------------------------------------------------
TEST1_libcheck_regularised.pdb
Description: Protein Databank data
