refinement with a covalent inhibitor.
Hi all, I am trying to refine a complex with a covalent inhibitor (E-64) that has a carboxylate group. My model has it planar, but after refinement the two oxygens of the carboxyl group get out of the plane. In the cif file generated by elbow this plane description is missing, I added it manually, but the result is the same. Maia
Hi Maia, Could you send us - your cif file - the part of the pdb file with the inhibitor residue and the residue it is bound to (if I understand correctly) - the beginning of the phenix.refine log file summarizing the processing of the pdb file ? Ralf
Hello Maia, Have you checked, if there are any wrong/weird hydrogens defined at your ligand? That can screw up your defined geometry. I usually use refmac to check my cifs, by running it using "structure idealisation" and "generate all hydrogens and output to coordinate file", putting in the coordinates of the ligand and the respect cif file. Than you will see, what is actually in your cif file. Maybe that helps Sabine Maia Cherney wrote:
Hi all, I am trying to refine a complex with a covalent inhibitor (E-64) that has a carboxylate group. My model has it planar, but after refinement the two oxygens of the carboxyl group get out of the plane. In the cif file generated by elbow this plane description is missing, I added it manually, but the result is the same.
Maia _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Sabine, I have checked all hydrogens that are produced by elbow in the elbow.ligand.pdb and they look fine. The carboxyl group has a hydrogen that has to be dissociated in a carboxylate. May be this is causing the problem. The best geometry I got for this ligand i got in CNS. HIC-Up server says 5 flat planes, but elbow finds only 2. Hopefully, Ralf will figure out the problem. Sabine Schneider wrote:
Hello Maia,
Have you checked, if there are any wrong/weird hydrogens defined at your ligand? That can screw up your defined geometry. I usually use refmac to check my cifs, by running it using "structure idealisation" and "generate all hydrogens and output to coordinate file", putting in the coordinates of the ligand and the respect cif file. Than you will see, what is actually in your cif file.
Maybe that helps
Sabine
Maia Cherney wrote:
Hi all, I am trying to refine a complex with a covalent inhibitor (E-64) that has a carboxylate group. My model has it planar, but after refinement the two oxygens of the carboxyl group get out of the plane. In the cif file generated by elbow this plane description is missing, I added it manually, but the result is the same.
Maia _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Maia Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar groups including the carboxyl group missing from the earlier PHENIX version I believe you used. I have attached it. There are a few other things I should mention. I used a tool called ReadySet! phenix.ready_set model.pdb which will generate (using eLBOW) CIF files for all the ligands in the model using the data from the Chemical Components database from the PDB. I would recommend that you use ReadySet! for preparing a PDB file for refinement. It also adds hydrogens to your model which is usually a good thing. Your example does have some nuances. You mention that it is covalently bound to the CYS. I have attached the two additional files needed to inform phenix.refine of the covalent bond. I used eLBOW directly for this but will ensure that ReadySet! will do the same function in the next release. An additional function that I have been working on recently is the removal of the hydrogen in a carboxyl group when the ligand is in the model. I shall have that in the next PHENIX release. Finally, I did a refinement using dummy reflection data and the carboxyl group remained planar. If you have any problems with any of the files, feel free to contact me directly. Nigel -- Nigel W. Moriarty, Ph.D. Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov # data_link_E64-CYS # 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 E64-CYS 1 C2 2 SG coval 1.816344 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 E64-CYS 1 C3 1 C2 2 SG 109.000000 3.000 E64-CYS 1 C2 2 SG 2 CB 109.000000 3.000 # # The following edits statement is similar to the apply_cif_link # command below. Uncomment the edits and comment the apply_cif_link # if desired. The CIF statments for the apply_cif_link are in the # corresponding ligand CIF file. # #refinement.geometry_restraints.edits { # bond { # action = *add # atom_selection_1 = name C2 and chain D and resname E64 and resseq 1 # atom_selection_2 = name SG and chain A and resname CYS and resseq 25 # distance_ideal = 1.816344 # sigma = 0.01 # } #} # refinement.pdb_interpretation.apply_cif_link { data_link = E64-CYS residue_selection_1 = chain D and resname E64 and resseq 1 residue_selection_2 = chain A and resname CYS and resseq 25 } # 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 E64 E64 ' ' ligand 55 25 . # data_comp_E64 # 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 E64 C9 C CH3 . -4.5730 -0.5881 3.2979 E64 C8 C CH1 . -3.0488 -0.6032 3.4181 E64 C10 C CH3 . -2.5451 -0.7502 4.8708 E64 C7 C CH2 . -2.3411 -1.5539 2.4017 E64 C6 C CH1 . -1.8454 -0.9451 1.0834 E64 N1 N NH1 . -2.2956 -1.6456 -0.1411 E64 C4 C C . -1.9707 -3.0615 -0.3461 E64 O4 O O . -1.3083 -3.6366 0.4434 E64 C3 C CH1 . -2.4783 -3.7844 -1.5829 E64 O3 O OH1 . -1.7907 -3.4475 -2.7749 E64 C2 C CH2 . -2.6236 -5.2739 -1.3882 E64 C1 C C . -3.1134 -6.1066 -2.5898 E64 O2 O OH1 . -2.3326 -6.9314 -3.1485 E64 O1 O O . -4.3044 -5.9894 -2.9960 E64 C11 C C . -0.3627 -0.5099 1.1289 E64 O5 O O . 0.3346 -0.8801 2.0164 E64 N2 N NH1 . 0.1635 0.4394 0.1222 E64 C12 C CH2 . 1.6048 0.8072 0.1124 E64 C13 C CH2 . 2.0181 2.0758 -0.7007 E64 C14 C CH2 . 3.4918 2.5475 -0.6205 E64 C15 C CH2 . 3.8723 3.8484 -1.3741 E64 N3 N NC1 . 5.2753 4.3126 -1.2842 E64 C16 C C . 5.7111 5.5132 -2.0257 E64 N4 N NC2 . 4.7397 6.2889 -2.7896 E64 N5 N NC2 . 6.9109 5.9447 -1.8962 E64 H6 H HCH1 . -2.3798 -0.0038 1.0149 E64 H3 H HCH1 . -3.4868 -3.4198 -1.7155 E64 H91 H HCH3 . -4.9668 -1.5859 3.5001 E64 H92 H HCH3 . -4.8530 -0.2853 2.2966 E64 H93 H HCH3 . -4.9845 0.1194 4.0189 E64 H8 H HCH1 . -2.7430 0.3916 3.1211 E64 H101 H HCH3 . -1.4849 -0.5374 4.9091 E64 H102 H HCH3 . -3.0773 -0.0511 5.5124 E64 H103 H HCH3 . -2.7228 -1.7566 5.2133 E64 H71 H HCH2 . -3.0338 -2.3517 2.1563 E64 H72 H HCH2 . -1.4829 -1.9977 2.9044 E64 HN1 H HNH1 . -2.8591 -1.1612 -0.8156 E64 HO3 H HOH1 . -2.4172 -3.2133 -3.4476 E64 H21 H HCH2 . -3.3187 -5.4350 -0.5712 E64 H22 H HCH2 . -1.6615 -5.6605 -1.0861 E64 HO2 H HOH1 . -2.8171 -7.4501 -3.7812 E64 HN2 H HNH1 . -0.4252 0.7451 -0.6187 E64 H121 H HCH2 . 1.9223 0.9543 1.1441 E64 H122 H HCH2 . 2.1609 -0.0468 -0.2954 E64 H131 H HCH2 . 1.7939 1.8836 -1.7403 E64 H132 H HCH2 . 1.3944 2.8931 -0.3718 E64 H141 H HCH2 . 4.1158 1.7520 -1.0055 E64 H142 H HCH2 . 3.7339 2.6870 0.4234 E64 H151 H HCH2 . 3.6409 3.7026 -2.4305 E64 H152 H HCH2 . 3.2358 4.6387 -0.9979 E64 HN3 H HNC1 . 5.9199 3.8343 -0.6935 E64 HN41 H HNC2 . 5.0390 7.0959 -3.3110 E64 HN42 H HNC2 . 3.7762 6.0150 -2.8000 E64 HN51 H HNC2 . 7.5846 5.4120 -1.3649 E64 HN52 H HNC2 . 7.2086 6.7613 -2.4048 # 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 E64 C8 C9 single 1.529 0.02 E64 C10 C8 single 1.545 0.02 E64 C7 C8 single 1.561 0.02 E64 C6 C7 single 1.534 0.02 E64 C4 N1 single 1.467 0.02 E64 O4 C4 double 1.180 0.02 E64 C3 C4 single 1.520 0.02 E64 O3 C3 single 1.417 0.02 E64 C2 C3 single 1.509 0.02 E64 C1 C2 single 1.542 0.02 E64 O2 C1 single 1.266 0.02 E64 O1 C1 double 1.264 0.02 E64 N1 C6 single 1.481 0.02 E64 C11 C6 single 1.546 0.02 E64 O5 C11 double 1.188 0.02 E64 N2 C11 single 1.480 0.02 E64 C12 N2 single 1.488 0.02 E64 C13 C12 single 1.562 0.02 E64 C14 C13 single 1.549 0.02 E64 C15 C14 single 1.551 0.02 E64 N3 C15 single 1.481 0.02 E64 C16 N3 single 1.477 0.02 E64 N4 C16 single 1.459 0.02 E64 N5 C16 double 1.282 0.02 E64 H6 C6 single 1.085 0.02 E64 H3 C3 single 1.081 0.02 E64 H91 C9 single 1.092 0.02 E64 H92 C9 single 1.083 0.02 E64 H93 C9 single 1.091 0.02 E64 H8 C8 single 1.082 0.02 E64 H101 C10 single 1.082 0.02 E64 H102 C10 single 1.088 0.02 E64 H103 C10 single 1.078 0.02 E64 H71 C7 single 1.085 0.02 E64 H72 C7 single 1.089 0.02 E64 HN1 N1 single 1.004 0.02 E64 HO3 O3 single 0.949 0.02 E64 H21 C2 single 1.085 0.02 E64 H22 C2 single 1.080 0.02 E64 HO2 O2 single 0.951 0.02 E64 HN2 N2 single 0.994 0.02 E64 H121 C12 single 1.090 0.02 E64 H122 C12 single 1.098 0.02 E64 H131 C13 single 1.081 0.02 E64 H132 C13 single 1.079 0.02 E64 H141 C14 single 1.082 0.02 E64 H142 C14 single 1.081 0.02 E64 H151 C15 single 1.091 0.02 E64 H152 C15 single 1.082 0.02 E64 HN3 N3 single 0.997 0.02 E64 HN41 N4 single 1.006 0.02 E64 HN42 N4 single 1.002 0.02 E64 HN51 N5 single 1.010 0.02 E64 HN52 N5 single 1.007 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 E64 C10 C8 C9 113.58 3.0 E64 C7 C8 C9 114.00 3.0 E64 C6 C7 C8 117.65 3.0 E64 C7 C8 C10 113.98 3.0 E64 N1 C6 C7 115.12 3.0 E64 C11 C6 C7 113.34 3.0 E64 H6 C6 C7 103.85 3.0 E64 C4 N1 C6 120.32 3.0 E64 O5 C11 C6 119.82 3.0 E64 N2 C11 C6 120.09 3.0 E64 O4 C4 N1 120.07 3.0 E64 C3 C4 N1 119.92 3.0 E64 C11 C6 N1 116.68 3.0 E64 H6 C6 N1 102.04 3.0 E64 O3 C3 C4 114.17 3.0 E64 C2 C3 C4 113.36 3.0 E64 H3 C3 C4 104.54 3.0 E64 C3 C4 O4 120.01 3.0 E64 C1 C2 C3 117.58 3.0 E64 C2 C3 O3 112.95 3.0 E64 H3 C3 O3 105.64 3.0 E64 H3 C3 C2 105.01 3.0 E64 O2 C1 C2 120.00 3.0 E64 O1 C1 C2 119.99 3.0 E64 O1 C1 O2 119.99 3.0 E64 H6 C6 C11 103.31 3.0 E64 C12 N2 C11 120.49 3.0 E64 N2 C11 O5 119.96 3.0 E64 C13 C12 N2 117.42 3.0 E64 C14 C13 C12 118.15 3.0 E64 C15 C14 C13 117.62 3.0 E64 N3 C15 C14 117.78 3.0 E64 C16 N3 C15 120.27 3.0 E64 N4 C16 N3 119.91 3.0 E64 N5 C16 N3 119.95 3.0 E64 N5 C16 N4 119.82 3.0 E64 H8 C8 C9 104.54 3.0 E64 H91 C9 C8 109.64 3.0 E64 H92 C9 C8 109.46 3.0 E64 H93 C9 C8 109.30 3.0 E64 H101 C10 C8 109.52 3.0 E64 H102 C10 C8 109.50 3.0 E64 H103 C10 C8 109.51 3.0 E64 H71 C7 C8 107.80 3.0 E64 H72 C7 C8 107.75 3.0 E64 H8 C8 C10 104.68 3.0 E64 H8 C8 C7 104.66 3.0 E64 H71 C7 C6 107.68 3.0 E64 H72 C7 C6 107.68 3.0 E64 HN1 N1 C6 119.88 3.0 E64 HN1 N1 C4 119.75 3.0 E64 HO3 O3 C3 109.56 3.0 E64 H21 C2 C3 107.78 3.0 E64 H22 C2 C3 107.68 3.0 E64 H21 C2 C1 107.65 3.0 E64 H22 C2 C1 107.92 3.0 E64 HO2 O2 C1 109.56 3.0 E64 HN2 N2 C11 119.57 3.0 E64 H121 C12 N2 108.03 3.0 E64 H122 C12 N2 107.52 3.0 E64 HN2 N2 C12 119.51 3.0 E64 H131 C13 C12 107.53 3.0 E64 H132 C13 C12 107.66 3.0 E64 H121 C12 C13 107.82 3.0 E64 H122 C12 C13 107.72 3.0 E64 H141 C14 C13 107.84 3.0 E64 H142 C14 C13 107.60 3.0 E64 H131 C13 C14 107.53 3.0 E64 H132 C13 C14 107.66 3.0 E64 H151 C15 C14 107.84 3.0 E64 H152 C15 C14 107.42 3.0 E64 H141 C14 C15 107.59 3.0 E64 H142 C14 C15 107.83 3.0 E64 HN3 N3 C15 119.90 3.0 E64 H151 C15 N3 107.56 3.0 E64 H152 C15 N3 107.89 3.0 E64 HN3 N3 C16 119.79 3.0 E64 HN41 N4 C16 119.97 3.0 E64 HN42 N4 C16 120.03 3.0 E64 HN51 N5 C16 120.01 3.0 E64 HN52 N5 C16 119.92 3.0 E64 H92 C9 H91 109.49 3.0 E64 H93 C9 H91 109.53 3.0 E64 H93 C9 H92 109.41 3.0 E64 H102 C10 H101 109.39 3.0 E64 H103 C10 H101 109.51 3.0 E64 H103 C10 H102 109.39 3.0 E64 H72 C7 H71 107.94 3.0 E64 H22 C2 H21 107.88 3.0 E64 H122 C12 H121 108.01 3.0 E64 H132 C13 H131 107.93 3.0 E64 H142 C14 H141 108.03 3.0 E64 H152 C15 H151 108.02 3.0 E64 HN42 N4 HN41 120.00 3.0 E64 HN52 N5 HN51 119.75 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 E64 Var_01 C6 C7 C8 C9 94.38 30.0 2 E64 Var_02 N1 C6 C7 C8 -127.80 30.0 1 E64 Var_03 C11 C6 C7 C8 94.25 30.0 1 E64 Var_04 H6 C6 C7 C8 -17.13 30.0 1 E64 Var_05 C6 C7 C8 C10 -132.99 30.0 2 E64 Var_06 C4 N1 C6 C7 -58.73 30.0 2 E64 Var_07 O5 C11 C6 C7 13.95 30.0 3 E64 Var_08 N2 C11 C6 C7 -161.85 30.0 3 E64 Var_09 O3 C3 C4 N1 74.70 30.0 1 E64 Var_10 C2 C3 C4 N1 -154.04 30.0 1 E64 Var_11 H3 C3 C4 N1 -40.24 30.0 1 E64 Var_12 C11 C6 N1 C4 77.78 30.0 3 E64 Var_13 H6 C6 N1 C4 -170.47 30.0 3 E64 Var_14 C1 C2 C3 C4 -179.15 30.0 1 E64 Var_15 O3 C3 C4 O4 -104.78 30.0 1 E64 Var_16 C2 C3 C4 O4 26.48 30.0 1 E64 Var_17 H3 C3 C4 O4 140.28 30.0 1 E64 Var_18 O2 C1 C2 C3 112.63 30.0 2 E64 Var_19 O1 C1 C2 C3 -69.12 30.0 2 E64 Var_20 C1 C2 C3 O3 -47.28 30.0 1 E64 Var_21 H3 C3 C2 C1 67.34 30.0 3 E64 Var_22 C13 C12 N2 C11 -163.90 30.0 1 E64 Var_23 H6 C6 C11 O5 125.67 30.0 3 E64 Var_24 H6 C6 C11 N2 -50.13 30.0 3 E64 Var_25 C14 C13 C12 N2 174.65 30.0 1 E64 Var_26 C15 C14 C13 C12 -176.97 30.0 1 E64 Var_27 N3 C15 C14 C13 179.16 30.0 1 E64 Var_28 C16 N3 C15 C14 177.45 30.0 1 E64 Var_29 H101 C10 C8 C9 -167.68 30.0 3 E64 Var_30 H102 C10 C8 C9 -47.72 30.0 3 E64 Var_31 H103 C10 C8 C9 72.22 30.0 3 E64 Var_32 H71 C7 C8 C9 -27.51 30.0 2 E64 Var_33 H72 C7 C8 C9 -143.77 30.0 2 E64 Var_34 H91 C9 C8 C10 -71.21 30.0 3 E64 Var_35 H92 C9 C8 C10 168.67 30.0 3 E64 Var_36 H93 C9 C8 C10 48.86 30.0 3 E64 Var_37 H71 C7 C8 C10 105.12 30.0 2 E64 Var_38 H72 C7 C8 C10 -11.14 30.0 2 E64 Var_39 H91 C9 C8 C7 61.61 30.0 3 E64 Var_40 H92 C9 C8 C7 -58.51 30.0 3 E64 Var_41 H93 C9 C8 C7 -178.32 30.0 3 E64 Var_42 H101 C10 C8 C7 59.50 30.0 3 E64 Var_43 H102 C10 C8 C7 179.45 30.0 3 E64 Var_44 H103 C10 C8 C7 -60.61 30.0 3 E64 Var_45 HN1 N1 C6 C7 118.62 30.0 2 E64 Var_46 H8 C8 C7 C6 -19.22 30.0 3 E64 Var_47 H71 C7 C6 N1 -5.84 30.0 3 E64 Var_48 H72 C7 C6 N1 110.32 30.0 3 E64 Var_49 HO3 O3 C3 C4 -129.18 30.0 3 E64 Var_50 H21 C2 C3 C4 59.06 30.0 1 E64 Var_51 H22 C2 C3 C4 -57.08 30.0 1 E64 Var_52 H21 C2 C3 O3 -169.08 30.0 1 E64 Var_53 H22 C2 C3 O3 74.78 30.0 1 E64 Var_54 HO3 O3 C3 C2 99.36 30.0 3 E64 Var_55 H21 C2 C1 O2 -125.51 30.0 3 E64 Var_56 H22 C2 C1 O2 -9.31 30.0 3 E64 Var_57 H21 C2 C1 O1 52.75 30.0 3 E64 Var_58 H22 C2 C1 O1 168.95 30.0 3 E64 Var_59 H71 C7 C6 C11 -143.79 30.0 3 E64 Var_60 H72 C7 C6 C11 -27.63 30.0 3 E64 Var_61 HN1 N1 C6 C11 -104.87 30.0 2 E64 Var_62 H121 C12 N2 C11 -41.80 30.0 1 E64 Var_63 H122 C12 N2 C11 74.54 30.0 1 E64 Var_64 H131 C13 C12 N2 -63.53 30.0 1 E64 Var_65 H132 C13 C12 N2 52.54 30.0 1 E64 Var_66 H141 C14 C13 C12 61.24 30.0 1 E64 Var_67 H142 C14 C13 C12 -55.07 30.0 1 E64 Var_68 HN2 N2 C12 C13 23.66 30.0 3 E64 Var_69 H151 C15 C14 C13 -59.00 30.0 1 E64 Var_70 H152 C15 C14 C13 57.21 30.0 1 E64 Var_71 H121 C12 C13 C14 52.44 30.0 3 E64 Var_72 H122 C12 C13 C14 -63.90 30.0 3 E64 Var_73 HN3 N3 C15 C14 -4.93 30.0 1 E64 Var_74 H131 C13 C14 C15 61.20 30.0 3 E64 Var_75 H132 C13 C14 C15 -54.86 30.0 3 E64 Var_76 H141 C14 C15 N3 -58.92 30.0 3 E64 Var_77 H142 C14 C15 N3 57.38 30.0 3 E64 Var_78 H151 C15 N3 C16 55.46 30.0 3 E64 Var_79 H152 C15 N3 C16 -60.84 30.0 3 E64 Var_80 H71 C7 C6 H6 104.82 30.0 3 E64 Var_81 H72 C7 C6 H6 -139.01 30.0 3 E64 Var_82 HN1 N1 C6 H6 6.88 30.0 2 E64 Var_83 HO3 O3 C3 H3 -14.89 30.0 3 E64 Var_84 H21 C2 C3 H3 -54.45 30.0 1 E64 Var_85 H22 C2 C3 H3 -170.60 30.0 1 E64 Var_86 H8 C8 C9 H91 175.28 30.0 3 E64 Var_87 H8 C8 C9 H92 55.16 30.0 3 E64 Var_88 H8 C8 C9 H93 -64.65 30.0 3 E64 Var_89 H101 C10 C8 H8 -54.26 30.0 3 E64 Var_90 H102 C10 C8 H8 65.70 30.0 3 E64 Var_91 H103 C10 C8 H8 -174.36 30.0 3 E64 Var_92 H71 C7 C8 H8 -141.12 30.0 2 E64 Var_93 H72 C7 C8 H8 102.63 30.0 2 E64 Var_94 H121 C12 N2 HN2 145.76 30.0 1 E64 Var_95 H122 C12 N2 HN2 -97.90 30.0 1 E64 Var_96 H131 C13 C12 H121 174.27 30.0 1 E64 Var_97 H132 C13 C12 H121 -69.67 30.0 1 E64 Var_98 H131 C13 C12 H122 57.93 30.0 1 E64 Var_99 H132 C13 C12 H122 174.00 30.0 1 E64 Var_100 H141 C14 C13 H131 -60.59 30.0 1 E64 Var_101 H142 C14 C13 H131 -176.90 30.0 1 E64 Var_102 H141 C14 C13 H132 -176.65 30.0 1 E64 Var_103 H142 C14 C13 H132 67.04 30.0 1 E64 Var_104 H151 C15 C14 H141 62.92 30.0 1 E64 Var_105 H152 C15 C14 H141 179.13 30.0 1 E64 Var_106 H151 C15 C14 H142 179.22 30.0 1 E64 Var_107 H152 C15 C14 H142 -64.57 30.0 1 E64 Var_108 HN3 N3 C15 H151 -126.92 30.0 1 E64 Var_109 HN3 N3 C15 H152 116.77 30.0 1 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 E64 chir_01 C6 C7 N1 C11 positiv E64 chir_02 C3 C4 O3 C2 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 E64 plan-1 C6 0.100 E64 plan-1 N1 0.100 E64 plan-1 C4 0.100 E64 plan-1 O4 0.100 E64 plan-1 C3 0.100 E64 plan-1 HN1 0.100 E64 plan-2 C6 0.100 E64 plan-2 N1 0.100 E64 plan-2 C11 0.100 E64 plan-2 O5 0.100 E64 plan-2 N2 0.100 E64 plan-2 C12 0.100 E64 plan-2 HN2 0.100 E64 plan-3 C15 0.100 E64 plan-3 N3 0.100 E64 plan-3 C16 0.100 E64 plan-3 N4 0.100 E64 plan-3 N5 0.100 E64 plan-3 HN3 0.100 E64 plan-3 HN41 0.100 E64 plan-3 HN42 0.100 E64 plan-3 HN51 0.100 E64 plan-3 HN52 0.100 E64 plan-4 C2 0.100 E64 plan-4 C1 0.100 E64 plan-4 O2 0.100 E64 plan-4 O1 0.100 E64 plan-4 HO2 0.100
Thank you Nigel, However, your cif file did not help with the problem (carboxylate is not planar) when using the PHENIX 1.4-3 version that we have now. You mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to get them both? By the way, phenix.ready_set (in our current version) screwed up all hydrogens in my other ligand (trimer of ASG-GCU). I think that the ready.set needs to know that the monomers are linked. With this particular ligand that is a hexamer, ASG is in the library, but GCU is not. Should I give a cif_link file for the ready.set, too? After I get a newer version of phenix, I 'll try it again. Maia Nigel W Moriarty wrote:
Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar groups including the carboxyl group missing from the earlier PHENIX version I believe you used. I have attached it. There are a few other things I should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the model using the data from the Chemical Components database from the PDB. I would recommend that you use ReadySet! for preparing a PDB file for refinement. It also adds hydrogens to your model which is usually a good thing.
Your example does have some nuances. You mention that it is covalently bound to the CYS. I have attached the two additional files needed to inform phenix.refine of the covalent bond. I used eLBOW directly for this but will ensure that ReadySet! will do the same function in the next release.
An additional function that I have been working on recently is the removal of the hydrogen in a carboxyl group when the ligand is in the model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the carboxyl group remained planar.
If you have any problems with any of the files, feel free to contact me directly.
Nigel
------------------------------------------------------------------------
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Maia Yes, please do download the latest PHENIX version and run ReadySet! again. To ensure that the ASG-GCU complex is handled correctly, you should put in the CONECT records into the PDB file that link the two "residues" in your ligand complex together. This is a rather complex example and I'd be interested in seeing your PDB file. Nigel On 3/17/09 3:10 PM, Maia Cherney wrote:
Thank you Nigel, However, your cif file did not help with the problem (carboxylate is not planar) when using the PHENIX 1.4-3 version that we have now. You mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to get them both? By the way, phenix.ready_set (in our current version) screwed up all hydrogens in my other ligand (trimer of ASG-GCU). I think that the ready.set needs to know that the monomers are linked. With this particular ligand that is a hexamer, ASG is in the library, but GCU is not. Should I give a cif_link file for the ready.set, too? After I get a newer version of phenix, I 'll try it again. Maia
Nigel W Moriarty wrote:
Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar groups including the carboxyl group missing from the earlier PHENIX version I believe you used. I have attached it. There are a few other things I should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the model using the data from the Chemical Components database from the PDB. I would recommend that you use ReadySet! for preparing a PDB file for refinement. It also adds hydrogens to your model which is usually a good thing.
Your example does have some nuances. You mention that it is covalently bound to the CYS. I have attached the two additional files needed to inform phenix.refine of the covalent bond. I used eLBOW directly for this but will ensure that ReadySet! will do the same function in the next release.
An additional function that I have been working on recently is the removal of the hydrogen in a carboxyl group when the ligand is in the model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the carboxyl group remained planar.
If you have any problems with any of the files, feel free to contact me directly.
Nigel
------------------------------------------------------------------------
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Hi Nigel, The native complex is published and in the PDB (code 3c9e). It was refined in CNS. It has all the ligands (E64, ASG-GCU and calcium2+) as in the mutant that I am working on now. If I still have the same problems with the newer version, I will send you my pdb, probably in a couple of days. Maia Nigel W Moriarty wrote:
Maia
Yes, please do download the latest PHENIX version and run ReadySet! again. To ensure that the ASG-GCU complex is handled correctly, you should put in the CONECT records into the PDB file that link the two "residues" in your ligand complex together. This is a rather complex example and I'd be interested in seeing your PDB file.
Nigel
On 3/17/09 3:10 PM, Maia Cherney wrote:
Thank you Nigel, However, your cif file did not help with the problem (carboxylate is not planar) when using the PHENIX 1.4-3 version that we have now. You mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to get them both? By the way, phenix.ready_set (in our current version) screwed up all hydrogens in my other ligand (trimer of ASG-GCU). I think that the ready.set needs to know that the monomers are linked. With this particular ligand that is a hexamer, ASG is in the library, but GCU is not. Should I give a cif_link file for the ready.set, too? After I get a newer version of phenix, I 'll try it again. Maia
Nigel W Moriarty wrote:
Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar groups including the carboxyl group missing from the earlier PHENIX version I believe you used. I have attached it. There are a few other things I should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the model using the data from the Chemical Components database from the PDB. I would recommend that you use ReadySet! for preparing a PDB file for refinement. It also adds hydrogens to your model which is usually a good thing.
Your example does have some nuances. You mention that it is covalently bound to the CYS. I have attached the two additional files needed to inform phenix.refine of the covalent bond. I used eLBOW directly for this but will ensure that ReadySet! will do the same function in the next release.
An additional function that I have been working on recently is the removal of the hydrogen in a carboxyl group when the ligand is in the model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the carboxyl group remained planar.
If you have any problems with any of the files, feel free to contact me directly.
Nigel
------------------------------------------------------------------------
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Hi Nigel, I can't find the newer phenix versions on the phenix home page. The latest version there is the same as I have now, 1.4-3! Where can I find the newer versions and why they are not on the phenix home page? Nigel W Moriarty wrote:
Maia
Yes, please do download the latest PHENIX version and run ReadySet! again. To ensure that the ASG-GCU complex is handled correctly, you should put in the CONECT records into the PDB file that link the two "residues" in your ligand complex together. This is a rather complex example and I'd be interested in seeing your PDB file.
Nigel
On 3/17/09 3:10 PM, Maia Cherney wrote:
Thank you Nigel, However, your cif file did not help with the problem (carboxylate is not planar) when using the PHENIX 1.4-3 version that we have now. You mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to get them both? By the way, phenix.ready_set (in our current version) screwed up all hydrogens in my other ligand (trimer of ASG-GCU). I think that the ready.set needs to know that the monomers are linked. With this particular ligand that is a hexamer, ASG is in the library, but GCU is not. Should I give a cif_link file for the ready.set, too? After I get a newer version of phenix, I 'll try it again. Maia
Nigel W Moriarty wrote:
Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar groups including the carboxyl group missing from the earlier PHENIX version I believe you used. I have attached it. There are a few other things I should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the model using the data from the Chemical Components database from the PDB. I would recommend that you use ReadySet! for preparing a PDB file for refinement. It also adds hydrogens to your model which is usually a good thing.
Your example does have some nuances. You mention that it is covalently bound to the CYS. I have attached the two additional files needed to inform phenix.refine of the covalent bond. I used eLBOW directly for this but will ensure that ReadySet! will do the same function in the next release.
An additional function that I have been working on recently is the removal of the hydrogen in a carboxyl group when the ligand is in the model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the carboxyl group remained planar.
If you have any problems with any of the files, feel free to contact me directly.
Nigel
------------------------------------------------------------------------
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov ------------------------------------------------------------------------
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Maia I took a look at the PDB entry 3C9E. The covalently bound ligand can be taken care of using the CIF link files. The chain of sugars is a different matter. There is a LINK to a symmetry copy such that the chain continues into the next ASU forming an infinite chain. I've started working on code to generate the needed files for refinement. If you need the files today, I can generated them with my test code and you can use them with the current version of PHENIX. Is the sugar chain the same as in 3C9E? Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Hi Nigel, Thank you for your help. The sugar chain is the same, but the crystal form is different and the sugar chain is not infinite, because a part of the chain is disordered. (To make the complex, I used a high molecular weight sugar, 17 or 30 KDa). Did you get the E64 carboxyl group flat? I have no trouble with covalent linking, just the geometry of the ligands. Do you need my pdb? Maia Nigel W Moriarty wrote:
Maia
I took a look at the PDB entry 3C9E. The covalently bound ligand can be taken care of using the CIF link files. The chain of sugars is a different matter. There is a LINK to a symmetry copy such that the chain continues into the next ASU forming an infinite chain. I've started working on code to generate the needed files for refinement. If you need the files today, I can generated them with my test code and you can use them with the current version of PHENIX.
Is the sugar chain the same as in 3C9E?
Nigel
Hi Nigel, I installed the phenix version 1.4-4 and now I get this error when running phenix.elbow model.pdb --do-all
Traceback (most recent call last): File "/raid/programs/linux/phenix-1.4-4/elbow/elbow/command_line/builder.py", line 1273, in <module> run() File "/raid/programs/linux/phenix-1.4-4/elbow/elbow/command_line/builder.py", line 1126, in run molecule = builder(molecule, options) File "/raid/programs/linux/phenix-1.4-4/elbow/elbow/command_line/builder.py", line 467, in builder verbose=(not options.silent), File "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/BondTopologyMixins.py", line 188, in Bondise self.CheckBondOrderWithoutHydrogens() File "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/BondTopologyMixins.py", line 1038, in CheckBondOrderWithoutHydrogens self.FlattenCNN() File "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/TopologyMixins.py", line 1741, in FlattenCNN rc = self.FlattenCNNOther(set_restraint_class=set_restraint_class) File "/raid/programs/linux/phenix-1.4-4/elbow/elbow/chemistry/TopologyMixins.py", line 1799, in FlattenCNNOther planes = self._cnn_planar_group(carbon, nitrogens) NameError: global name 'carbon' is not defined
Maia Nigel W Moriarty wrote:
Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar groups including the carboxyl group missing from the earlier PHENIX version I believe you used. I have attached it. There are a few other things I should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the model using the data from the Chemical Components database from the PDB. I would recommend that you use ReadySet! for preparing a PDB file for refinement. It also adds hydrogens to your model which is usually a good thing.
Your example does have some nuances. You mention that it is covalently bound to the CYS. I have attached the two additional files needed to inform phenix.refine of the covalent bond. I used eLBOW directly for this but will ensure that ReadySet! will do the same function in the next release.
An additional function that I have been working on recently is the removal of the hydrogen in a carboxyl group when the ligand is in the model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the carboxyl group remained planar.
If you have any problems with any of the files, feel free to contact me directly.
Nigel
------------------------------------------------------------------------
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participants (4)
-
Maia Cherney -
Nigel W Moriarty -
Ralf W. Grosse-Kunstleve -
Sabine Schneider