How do I make trisaccharide, tetrasaccharides
How do I make trisaccharide, tetrasaccharides, etc from single monosaccharides? I.e., how do I join the monosaccharides. Do I use ideal coordinates? Can I join them in coot? I want to make HBGA Trisaccharide B. That is, I want to join FUC-GAL-GLA, it would be FUC (C1)-GAL (O2)-GAL (C2) then GAL (C3)-GAL(O3)-GLA(C1) ATOM 1 C1 FUC A 1 1.410 0.468 -0.410 1.00 10.00 C ATOM 2 C2 FUC A 1 0.120 0.513 -1.233 1.00 10.00 C ATOM 3 C3 FUC A 1 -0.831 -0.576 -0.728 1.00 10.00 C ATOM 4 C4 FUC A 1 -1.016 -0.402 0.783 1.00 10.00 C ATOM 5 C5 FUC A 1 0.359 -0.379 1.454 1.00 10.00 C ATOM 6 C6 FUC A 1 0.185 -0.241 2.967 1.00 10.00 C ATOM 7 O1 FUC A 1 2.007 -0.823 -0.535 1.00 10.00 O ATOM 8 O2 FUC A 1 0.424 0.284 -2.610 1.00 10.00 O ATOM 9 O3 FUC A 1 -2.094 -0.452 -1.385 1.00 10.00 O ATOM 10 O4 FUC A 1 -1.700 0.824 1.044 1.00 10.00 O ATOM 11 O5 FUC A 1 1.116 0.724 0.961 1.00 10.00 O ATOM 1 C1 GAL A 1 1.384 0.161 -0.445 1.00 10.00 C ATOM 2 C2 GAL A 1 0.328 -0.139 -1.512 1.00 10.00 C ATOM 3 C3 GAL A 1 -0.975 0.575 -1.139 1.00 10.00 C ATOM 4 C4 GAL A 1 -1.360 0.176 0.289 1.00 10.00 C ATOM 5 C5 GAL A 1 -0.177 0.454 1.220 1.00 10.00 C ATOM 6 C6 GAL A 1 -0.563 0.093 2.655 1.00 10.00 C ATOM 7 O1 GAL A 1 2.612 -0.476 -0.802 1.00 10.00 O ATOM 8 O2 GAL A 1 0.785 0.328 -2.782 1.00 10.00 O ATOM 9 O3 GAL A 1 -2.011 0.186 -2.044 1.00 10.00 O ATOM 10 O4 GAL A 1 -1.686 -1.213 0.327 1.00 10.00 O ATOM 11 O5 GAL A 1 0.945 -0.328 0.819 1.00 10.00 O ATOM 12 O6 GAL A 1 0.539 0.355 3.526 1.00 10.00 O ATOM 1 C1 GLA A 1 1.424 -0.489 -0.382 1.00 10.00 C ATOM 2 C2 GLA A 1 0.392 -0.498 -1.512 1.00 10.00 C ATOM 3 C3 GLA A 1 -0.650 0.592 -1.244 1.00 10.00 C ATOM 4 C4 GLA A 1 -1.222 0.387 0.163 1.00 10.00 C ATOM 5 C5 GLA A 1 -0.068 0.330 1.166 1.00 10.00 C ATOM 6 C6 GLA A 1 -0.630 0.161 2.579 1.00 10.00 C ATOM 7 O1 GLA A 1 2.043 0.797 -0.316 1.00 10.00 O ATOM 8 O2 GLA A 1 1.044 -0.242 -2.757 1.00 10.00 O ATOM 9 O3 GLA A 1 -1.700 0.498 -2.209 1.00 10.00 O ATOM 10 O4 GLA A 1 -1.958 -0.836 0.206 1.00 10.00 O ATOM 11 O5 GLA A 1 0.783 -0.771 0.859 1.00 10.00 O ATOM 12 O6 GLA A 1 0.446 0.112 3.517 1.00 10.00 O
Hi, it's as easy as 1-2-3 -:) (I hope): - define custom bonds between corresponding atoms; - get CIF file (if necessary) (I guess you need it for GLA); - run phenix.refine without using X-ray term (geometry regularization only), and that will do exactly what you want. Please let me know if you need any help with this. Pavel. On 4/27/10 4:21 PM, Hansman, Grant (NIH/VRC) [F] wrote:
How do I make trisaccharide, tetrasaccharides, etc from single monosaccharides? I.e., how do I join the monosaccharides. Do I use ideal coordinates? Can I join them in coot? I want to make HBGA Trisaccharide B.
That is, I want to join FUC-GAL-GLA, it would be FUC (C1)-GAL (O2)-GAL (C2) then GAL (C3)-GAL(O3)-GLA(C1)
ATOM 1 C1 FUC A 1 1.410 0.468 -0.410 1.00 10.00 C
ATOM 2 C2 FUC A 1 0.120 0.513 -1.233 1.00 10.00 C
ATOM 3 C3 FUC A 1 -0.831 -0.576 -0.728 1.00 10.00 C
ATOM 4 C4 FUC A 1 -1.016 -0.402 0.783 1.00 10.00 C
ATOM 5 C5 FUC A 1 0.359 -0.379 1.454 1.00 10.00 C
ATOM 6 C6 FUC A 1 0.185 -0.241 2.967 1.00 10.00 C
ATOM 7 O1 FUC A 1 2.007 -0.823 -0.535 1.00 10.00 O
ATOM 8 O2 FUC A 1 0.424 0.284 -2.610 1.00 10.00 O
ATOM 9 O3 FUC A 1 -2.094 -0.452 -1.385 1.00 10.00 O
ATOM 10 O4 FUC A 1 -1.700 0.824 1.044 1.00 10.00 O
ATOM 11 O5 FUC A 1 1.116 0.724 0.961 1.00 10.00 O
ATOM 1 C1 GAL A 1 1.384 0.161 -0.445 1.00 10.00 C
ATOM 2 C2 GAL A 1 0.328 -0.139 -1.512 1.00 10.00 C
ATOM 3 C3 GAL A 1 -0.975 0.575 -1.139 1.00 10.00 C
ATOM 4 C4 GAL A 1 -1.360 0.176 0.289 1.00 10.00 C
ATOM 5 C5 GAL A 1 -0.177 0.454 1.220 1.00 10.00 C
ATOM 6 C6 GAL A 1 -0.563 0.093 2.655 1.00 10.00 C
ATOM 7 O1 GAL A 1 2.612 -0.476 -0.802 1.00 10.00 O
ATOM 8 O2 GAL A 1 0.785 0.328 -2.782 1.00 10.00 O
ATOM 9 O3 GAL A 1 -2.011 0.186 -2.044 1.00 10.00 O
ATOM 10 O4 GAL A 1 -1.686 -1.213 0.327 1.00 10.00 O
ATOM 11 O5 GAL A 1 0.945 -0.328 0.819 1.00 10.00 O
ATOM 12 O6 GAL A 1 0.539 0.355 3.526 1.00 10.00 O
ATOM 1 C1 GLA A 1 1.424 -0.489 -0.382 1.00 10.00 C
ATOM 2 C2 GLA A 1 0.392 -0.498 -1.512 1.00 10.00 C
ATOM 3 C3 GLA A 1 -0.650 0.592 -1.244 1.00 10.00 C
ATOM 4 C4 GLA A 1 -1.222 0.387 0.163 1.00 10.00 C
ATOM 5 C5 GLA A 1 -0.068 0.330 1.166 1.00 10.00 C
ATOM 6 C6 GLA A 1 -0.630 0.161 2.579 1.00 10.00 C
ATOM 7 O1 GLA A 1 2.043 0.797 -0.316 1.00 10.00 O
ATOM 8 O2 GLA A 1 1.044 -0.242 -2.757 1.00 10.00 O
ATOM 9 O3 GLA A 1 -1.700 0.498 -2.209 1.00 10.00 O
ATOM 10 O4 GLA A 1 -1.958 -0.836 0.206 1.00 10.00 O
ATOM 11 O5 GLA A 1 0.783 -0.771 0.859 1.00 10.00 O
ATOM 12 O6 GLA A 1 0.446 0.112 3.517 1.00 10.00 O
------------------------------------------------------------------------
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Here it is, step-by-step: 1) Create a PDB file with FUC, GAL, GLA (copy-paste from your email), zz.pdb, renumber residues (just to look nice); 2) Run phenix.refine --show_defaults=all > params and edit "params" file to define custom bonds; 3) Run phenix.ready_set zz.pdb to get zz.cif file for GLA 4) Add dummy CRYST1 record to zz.pdb 5) Create dummy set of "Fobs": phenix.fmodel zz.pdb high_res=3 label=f-obs r_free=0.1 type=real output.file_name=zz.mtz 6) Run phenix.refine to idealize the geometry of zz.pdb: phenix.refine zz.{cif,pdb,mtz} strategy=individual_sites main.bulk_sol=false output.prefix=zz_idealized params refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None main.number_of_mac=50 --overwrite The file zz_idealized_001.pdb is the answer. All above mentioned files are here: http://cci.lbl.gov/~afonine/tmp2/ Let me know if you have any questions. Pavel. PS> It will be much easier to do in future -:) On 4/27/10 4:21 PM, Hansman, Grant (NIH/VRC) [F] wrote:
How do I make trisaccharide, tetrasaccharides, etc from single monosaccharides? I.e., how do I join the monosaccharides. Do I use ideal coordinates? Can I join them in coot? I want to make HBGA Trisaccharide B.
That is, I want to join FUC-GAL-GLA, it would be FUC (C1)-GAL (O2)-GAL (C2) then GAL (C3)-GAL(O3)-GLA(C1)
ATOM 1 C1 FUC A 1 1.410 0.468 -0.410 1.00 10.00 C
ATOM 2 C2 FUC A 1 0.120 0.513 -1.233 1.00 10.00 C
ATOM 3 C3 FUC A 1 -0.831 -0.576 -0.728 1.00 10.00 C
ATOM 4 C4 FUC A 1 -1.016 -0.402 0.783 1.00 10.00 C
ATOM 5 C5 FUC A 1 0.359 -0.379 1.454 1.00 10.00 C
ATOM 6 C6 FUC A 1 0.185 -0.241 2.967 1.00 10.00 C
ATOM 7 O1 FUC A 1 2.007 -0.823 -0.535 1.00 10.00 O
ATOM 8 O2 FUC A 1 0.424 0.284 -2.610 1.00 10.00 O
ATOM 9 O3 FUC A 1 -2.094 -0.452 -1.385 1.00 10.00 O
ATOM 10 O4 FUC A 1 -1.700 0.824 1.044 1.00 10.00 O
ATOM 11 O5 FUC A 1 1.116 0.724 0.961 1.00 10.00 O
ATOM 1 C1 GAL A 1 1.384 0.161 -0.445 1.00 10.00 C
ATOM 2 C2 GAL A 1 0.328 -0.139 -1.512 1.00 10.00 C
ATOM 3 C3 GAL A 1 -0.975 0.575 -1.139 1.00 10.00 C
ATOM 4 C4 GAL A 1 -1.360 0.176 0.289 1.00 10.00 C
ATOM 5 C5 GAL A 1 -0.177 0.454 1.220 1.00 10.00 C
ATOM 6 C6 GAL A 1 -0.563 0.093 2.655 1.00 10.00 C
ATOM 7 O1 GAL A 1 2.612 -0.476 -0.802 1.00 10.00 O
ATOM 8 O2 GAL A 1 0.785 0.328 -2.782 1.00 10.00 O
ATOM 9 O3 GAL A 1 -2.011 0.186 -2.044 1.00 10.00 O
ATOM 10 O4 GAL A 1 -1.686 -1.213 0.327 1.00 10.00 O
ATOM 11 O5 GAL A 1 0.945 -0.328 0.819 1.00 10.00 O
ATOM 12 O6 GAL A 1 0.539 0.355 3.526 1.00 10.00 O
ATOM 1 C1 GLA A 1 1.424 -0.489 -0.382 1.00 10.00 C
ATOM 2 C2 GLA A 1 0.392 -0.498 -1.512 1.00 10.00 C
ATOM 3 C3 GLA A 1 -0.650 0.592 -1.244 1.00 10.00 C
ATOM 4 C4 GLA A 1 -1.222 0.387 0.163 1.00 10.00 C
ATOM 5 C5 GLA A 1 -0.068 0.330 1.166 1.00 10.00 C
ATOM 6 C6 GLA A 1 -0.630 0.161 2.579 1.00 10.00 C
ATOM 7 O1 GLA A 1 2.043 0.797 -0.316 1.00 10.00 O
ATOM 8 O2 GLA A 1 1.044 -0.242 -2.757 1.00 10.00 O
ATOM 9 O3 GLA A 1 -1.700 0.498 -2.209 1.00 10.00 O
ATOM 10 O4 GLA A 1 -1.958 -0.836 0.206 1.00 10.00 O
ATOM 11 O5 GLA A 1 0.783 -0.771 0.859 1.00 10.00 O
ATOM 12 O6 GLA A 1 0.446 0.112 3.517 1.00 10.00 O
------------------------------------------------------------------------
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Grant You can use the data links that are defined in the Monomer Library (or define them yourself). For example, the alpha 1-2 link is defined below. You need to create a file something like this refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-2 residue_selection_1 = chain A and resname GAL and resid 1 residue_selection_2 = chain A and resname FUC and resid 2 } and pass this to phenix.refine. I leave the details to you. You can read the glycosidic bond links in $PHENIX/chem_data/mon_lib/list/mon_lib_list.cif starting at line 4080. You can read more about linking at http://phenix-online.org/documentation/refinement.htm#anch78 Nigel data_link_ALPHA1-2 # 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 ALPHA1-2 1 O2 2 C1 single 1.439 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 ALPHA1-2 1 C2 1 O2 2 C1 108.700 3.000 ALPHA1-2 1 O2 2 C1 2 O5 112.300 3.000 ALPHA1-2 1 O2 2 C1 2 C2 109.470 3.000 ALPHA1-2 1 O2 2 C1 2 H1 109.470 3.000 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 ALPHA1-2 ALPHA_1 1 O2 2 C1 2 C2 2 C3 0.00 20.0 1 ALPHA1-2 ALPHA_2 1 C2 1 O2 2 C1 2 C2 0.00 20.0 1 ALPHA1-2 ALPHA_3 1 C1 1 C2 1 O2 2 C1 0.00 20.0 1 loop_ _chem_link_chir.link_id _chem_link_chir.atom_centre_comp_id _chem_link_chir.atom_id_centre _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.volume_sign ALPHA1-2 2 C1 1 O2 2 O5 2 C2 negativ On 4/27/10 4:21 PM, Hansman, Grant (NIH/VRC) [F] wrote:
How do I make trisaccharide, tetrasaccharides, etc from single monosaccharides? I.e., how do I join the monosaccharides. Do I use ideal coordinates? Can I join them in coot? I want to make HBGA Trisaccharide B.
That is, I want to join FUC-GAL-GLA, it would be FUC (C1)-GAL (O2)-GAL (C2) then GAL (C3)-GAL(O3)-GLA(C1)
ATOM 1 C1 FUC A 1 1.410 0.468 -0.410 1.00 10.00 C
ATOM 2 C2 FUC A 1 0.120 0.513 -1.233 1.00 10.00 C
ATOM 3 C3 FUC A 1 -0.831 -0.576 -0.728 1.00 10.00 C
ATOM 4 C4 FUC A 1 -1.016 -0.402 0.783 1.00 10.00 C
ATOM 5 C5 FUC A 1 0.359 -0.379 1.454 1.00 10.00 C
ATOM 6 C6 FUC A 1 0.185 -0.241 2.967 1.00 10.00 C
ATOM 7 O1 FUC A 1 2.007 -0.823 -0.535 1.00 10.00 O
ATOM 8 O2 FUC A 1 0.424 0.284 -2.610 1.00 10.00 O
ATOM 9 O3 FUC A 1 -2.094 -0.452 -1.385 1.00 10.00 O
ATOM 10 O4 FUC A 1 -1.700 0.824 1.044 1.00 10.00 O
ATOM 11 O5 FUC A 1 1.116 0.724 0.961 1.00 10.00 O
ATOM 1 C1 GAL A 1 1.384 0.161 -0.445 1.00 10.00 C
ATOM 2 C2 GAL A 1 0.328 -0.139 -1.512 1.00 10.00 C
ATOM 3 C3 GAL A 1 -0.975 0.575 -1.139 1.00 10.00 C
ATOM 4 C4 GAL A 1 -1.360 0.176 0.289 1.00 10.00 C
ATOM 5 C5 GAL A 1 -0.177 0.454 1.220 1.00 10.00 C
ATOM 6 C6 GAL A 1 -0.563 0.093 2.655 1.00 10.00 C
ATOM 7 O1 GAL A 1 2.612 -0.476 -0.802 1.00 10.00 O
ATOM 8 O2 GAL A 1 0.785 0.328 -2.782 1.00 10.00 O
ATOM 9 O3 GAL A 1 -2.011 0.186 -2.044 1.00 10.00 O
ATOM 10 O4 GAL A 1 -1.686 -1.213 0.327 1.00 10.00 O
ATOM 11 O5 GAL A 1 0.945 -0.328 0.819 1.00 10.00 O
ATOM 12 O6 GAL A 1 0.539 0.355 3.526 1.00 10.00 O
ATOM 1 C1 GLA A 1 1.424 -0.489 -0.382 1.00 10.00 C
ATOM 2 C2 GLA A 1 0.392 -0.498 -1.512 1.00 10.00 C
ATOM 3 C3 GLA A 1 -0.650 0.592 -1.244 1.00 10.00 C
ATOM 4 C4 GLA A 1 -1.222 0.387 0.163 1.00 10.00 C
ATOM 5 C5 GLA A 1 -0.068 0.330 1.166 1.00 10.00 C
ATOM 6 C6 GLA A 1 -0.630 0.161 2.579 1.00 10.00 C
ATOM 7 O1 GLA A 1 2.043 0.797 -0.316 1.00 10.00 O
ATOM 8 O2 GLA A 1 1.044 -0.242 -2.757 1.00 10.00 O
ATOM 9 O3 GLA A 1 -1.700 0.498 -2.209 1.00 10.00 O
ATOM 10 O4 GLA A 1 -1.958 -0.836 0.206 1.00 10.00 O
ATOM 11 O5 GLA A 1 0.783 -0.771 0.859 1.00 10.00 O
ATOM 12 O6 GLA A 1 0.446 0.112 3.517 1.00 10.00 O
------------------------------------------------------------------------
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
participants (3)
-
Hansman, Grant (NIH/VRC) [F] -
Nigel W Moriarty -
Pavel Afonine