leonarski_f
63f5f96132
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* Rugnux: A placed model is refined by default - restrained maximum-likelihood refinement on the GPU (CPU without one), writing `<prefix>_refined_model.cif`, `<prefix>_refined_maps.mtz` and the difference-map blobs in `<prefix>_blobs.json`; `--no-refine` skips it. * Rugnux: `--mode refine` refines a model against merged structure factors from an MTZ or mmCIF file. * Rugnux: The embedded restraint dictionary covers amino acids, nucleotides including common modified RNA nucleotides, common cofactors, crystallisation additives, waters and ions, with metal sites restrained from the model's LINK records. * Rugnux: A model or reference file can be given among the inputs in any order, recognised by its contents. * Rugnux: The geometry refinement algorithm option is now `-r, --geom-refine` (was `--refine`). * Rugnux: Serial stills resolve the indexing ambiguity from the data when no model or reference is given, reject merge outliers by default, follow the run's measured rocking curve in prediction and partiality (also in `--mode scale`), and index reproducibly on the GPU. * Rugnux: Reflections touching the beam-stop shadow are not integrated, reflections coarser than the low-resolution limit are merged and written (but kept out of the scale fit), and the polarisation plane is measured more reliably. * Rugnux: Small-molecule runs report unit-cell e.s.d.s, in a SHELX `.ins` beside the `.hkl` and in the mmCIF. * jfjoch_broker: Live Rugnux refines the uploaded model after placement; the web frontend's Rugnux live page has a hero panel with resolution, ISa, space group, placement and refined R-work/R-free, and its Mol* viewer shows the refined model and maps. * Documentation: A new front page with download pages for Rugnux and the viewer, and the technical reference reorganised below it. * Build: The fast-feedback indexer is part of the source tree instead of being downloaded at build time. Reviewed-on: #91 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
269 lines
7.3 KiB
Plaintext
269 lines
7.3 KiB
Plaintext
data_comp_list
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loop_
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_chem_comp.id
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_chem_comp.three_letter_code
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_chem_comp.name
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_chem_comp.group
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_chem_comp.number_atoms_all
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_chem_comp.number_atoms_nh
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_chem_comp.desc_level
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TYR TYR TYROSINE peptide 24 13 .
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data_comp_TYR
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loop_
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_chem_comp_atom.comp_id
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_chem_comp_atom.atom_id
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_chem_comp_atom.type_symbol
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_chem_comp_atom.type_energy
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_chem_comp_atom.charge
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_chem_comp_atom.x
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_chem_comp_atom.y
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_chem_comp_atom.z
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TYR N N NT3 1 5.311 5.160 15.589
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TYR CA C CH1 0 5.358 6.374 16.456
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TYR C C C 0 4.823 7.578 15.662
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TYR O O O 0 3.988 8.305 16.245
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TYR CB C CH2 0 6.763 6.679 16.994
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TYR CG C CR6 0 7.348 5.630 17.938
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TYR CD1 C CR16 0 7.096 5.672 19.314
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TYR CD2 C CR16 0 8.161 4.597 17.458
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TYR CE1 C CR16 0 7.628 4.720 20.176
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TYR CE2 C CR16 0 8.697 3.641 18.313
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TYR CZ C CR6 0 8.431 3.702 19.674
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TYR OH O OH1 0 8.982 2.738 20.476
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TYR OXT O OC -1 5.248 7.759 14.496
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TYR H H H 0 5.552 4.421 16.046
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TYR H2 H H 0 5.856 5.257 14.876
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TYR H3 H H 0 4.470 5.038 15.288
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TYR HA H H 0 4.756 6.220 17.232
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TYR HB3 H H 0 6.733 7.543 17.464
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TYR HB2 H H 0 7.369 6.788 16.227
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TYR HD1 H H 0 6.552 6.358 19.667
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TYR HD2 H H 0 8.350 4.543 16.534
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TYR HE1 H H 0 7.444 4.765 21.099
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TYR HE2 H H 0 9.240 2.953 17.971
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TYR HH H H 0 8.782 2.828 21.308
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loop_
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_chem_comp_tree.comp_id
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_chem_comp_tree.atom_id
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_chem_comp_tree.atom_back
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_chem_comp_tree.atom_forward
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_chem_comp_tree.connect_type
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TYR N n/a CA START
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TYR H N . .
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TYR H2 N . .
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TYR H3 N . .
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TYR CA N C .
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TYR HA CA . .
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TYR CB CA CG .
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TYR HB3 CB . .
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TYR HB2 CB . .
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TYR CG CB CD1 .
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TYR CD1 CG CE1 .
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TYR HD1 CD1 . .
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TYR CE1 CD1 CZ .
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TYR HE1 CE1 . .
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TYR CZ CE1 CE2 .
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TYR OH CZ HH .
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TYR HH OH . .
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TYR CE2 CZ CD2 .
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TYR HE2 CE2 . .
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TYR CD2 CE2 HD2 .
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TYR HD2 CD2 . .
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TYR C CA . END
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TYR O C . .
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TYR OXT C . .
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TYR CD2 CG . ADD
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loop_
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_chem_comp_acedrg.comp_id
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_chem_comp_acedrg.atom_id
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_chem_comp_acedrg.atom_type
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TYR N N(CCCH)(H)3
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TYR CA C(CC[6a]HH)(NH3)(COO)(H)
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TYR C C(CCHN)(O)2
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TYR O O(CCO)
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TYR CB C(C[6a]C[6a]2)(CCHN)(H)2
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TYR CG C[6a](C[6a]C[6a]H)2(CCHH){1|C<3>,2|H<1>}
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TYR CD1 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>}
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TYR CD2 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>}
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TYR CE1 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>}
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TYR CE2 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>}
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TYR CZ C[6a](C[6a]C[6a]H)2(OH){1|C<3>,2|H<1>}
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TYR OH O(C[6a]C[6a]2)(H)
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TYR OXT O(CCO)
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TYR H H(NCHH)
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TYR H2 H(NCHH)
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TYR H3 H(NCHH)
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TYR HA H(CCCN)
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TYR HB3 H(CC[6a]CH)
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TYR HB2 H(CC[6a]CH)
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TYR HD1 H(C[6a]C[6a]2)
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TYR HD2 H(C[6a]C[6a]2)
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TYR HE1 H(C[6a]C[6a]2)
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TYR HE2 H(C[6a]C[6a]2)
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TYR HH H(OC[6a])
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loop_
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_chem_comp_bond.comp_id
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_chem_comp_bond.atom_id_1
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_chem_comp_bond.atom_id_2
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_chem_comp_bond.type
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_chem_comp_bond.aromatic
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_chem_comp_bond.value_dist_nucleus
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_chem_comp_bond.value_dist_nucleus_esd
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_chem_comp_bond.value_dist
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_chem_comp_bond.value_dist_esd
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TYR N CA SINGLE n 1.489 0.0100 1.489 0.0100
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TYR CA C SINGLE n 1.531 0.0171 1.531 0.0171
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TYR CA CB SINGLE n 1.532 0.0100 1.532 0.0100
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TYR C O DOUBLE n 1.251 0.0183 1.251 0.0183
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TYR C OXT SINGLE n 1.251 0.0183 1.251 0.0183
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TYR CB CG SINGLE n 1.523 0.0100 1.523 0.0100
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TYR CG CD1 DOUBLE y 1.390 0.0116 1.390 0.0116
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TYR CG CD2 SINGLE y 1.390 0.0116 1.390 0.0116
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TYR CD1 CE1 SINGLE y 1.385 0.0100 1.385 0.0100
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TYR CD2 CE2 DOUBLE y 1.385 0.0100 1.385 0.0100
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TYR CE1 CZ DOUBLE y 1.383 0.0100 1.383 0.0100
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TYR CE2 CZ SINGLE y 1.383 0.0100 1.383 0.0100
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TYR CZ OH SINGLE n 1.365 0.0137 1.365 0.0137
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TYR N H SINGLE n 1.018 0.0520 0.902 0.0102
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TYR N H2 SINGLE n 1.018 0.0520 0.902 0.0102
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TYR N H3 SINGLE n 1.018 0.0520 0.902 0.0102
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TYR CA HA SINGLE n 1.092 0.0100 0.994 0.0200
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TYR CB HB3 SINGLE n 1.092 0.0100 0.983 0.0163
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TYR CB HB2 SINGLE n 1.092 0.0100 0.983 0.0163
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TYR CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0143
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TYR CD2 HD2 SINGLE n 1.085 0.0150 0.944 0.0143
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TYR CE1 HE1 SINGLE n 1.085 0.0150 0.942 0.0174
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TYR CE2 HE2 SINGLE n 1.085 0.0150 0.942 0.0174
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TYR OH HH SINGLE n 0.966 0.0059 0.858 0.0200
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loop_
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_chem_comp_angle.comp_id
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_chem_comp_angle.atom_id_1
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_chem_comp_angle.atom_id_2
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_chem_comp_angle.atom_id_3
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_chem_comp_angle.value_angle
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_chem_comp_angle.value_angle_esd
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TYR CA N H 109.791 3.00
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TYR CA N H2 109.791 3.00
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TYR CA N H3 109.791 3.00
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TYR H N H2 109.032 3.00
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TYR H N H3 109.032 3.00
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TYR H2 N H3 109.032 3.00
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TYR N CA C 109.085 1.50
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TYR N CA CB 109.965 3.00
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TYR N CA HA 108.547 1.50
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TYR C CA CB 111.980 3.00
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TYR C CA HA 108.746 1.50
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TYR CB CA HA 108.686 1.50
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TYR CA C O 117.219 3.00
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TYR CA C OXT 117.219 3.00
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TYR O C OXT 125.562 1.50
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TYR CA CB CG 114.693 2.05
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TYR CA CB HB3 108.494 1.50
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TYR CA CB HB2 108.494 1.50
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TYR CG CB HB3 108.859 1.50
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TYR CG CB HB2 108.859 1.50
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TYR HB3 CB HB2 107.843 2.16
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TYR CB CG CD1 121.060 1.50
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TYR CB CG CD2 121.060 1.50
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TYR CD1 CG CD2 117.879 1.50
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TYR CG CD1 CE1 121.468 1.50
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TYR CG CD1 HD1 119.327 1.50
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TYR CE1 CD1 HD1 119.205 1.50
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TYR CG CD2 CE2 121.468 1.50
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TYR CG CD2 HD2 119.327 1.50
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TYR CE2 CD2 HD2 119.205 1.50
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TYR CD1 CE1 CZ 119.794 1.50
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TYR CD1 CE1 HE1 120.177 1.50
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TYR CZ CE1 HE1 120.029 1.50
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TYR CD2 CE2 CZ 119.794 1.50
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TYR CD2 CE2 HE2 120.177 1.50
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TYR CZ CE2 HE2 120.029 1.50
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TYR CE1 CZ CE2 119.597 1.50
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TYR CE1 CZ OH 120.202 3.00
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TYR CE2 CZ OH 120.202 3.00
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TYR CZ OH HH 109.970 3.00
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loop_
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_chem_comp_tor.comp_id
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_chem_comp_tor.id
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_chem_comp_tor.atom_id_1
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_chem_comp_tor.atom_id_2
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_chem_comp_tor.atom_id_3
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_chem_comp_tor.atom_id_4
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_chem_comp_tor.value_angle
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_chem_comp_tor.value_angle_esd
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_chem_comp_tor.period
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TYR chi1 N CA CB CG -60.000 10.0 3
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TYR chi2 CA CB CG CD1 90.000 10.0 6
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TYR CONST_1 CB CG CD1 CE1 0.000 0.0 1
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TYR CONST_2 CG CD1 CE1 CZ 0.000 0.0 1
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TYR CONST_3 CZ CE2 CD2 CG 0.000 0.0 1
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TYR CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1
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TYR CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1
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TYR hh1 CE1 CZ OH HH 0.000 5.0 2
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TYR sp3_sp3_1 C CA N H 180.000 10.0 3
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TYR const_21 CE2 CD2 CG CD1 0.000 0.0 1
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TYR sp2_sp3_1 O C CA N 0.000 10.0 6
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loop_
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_chem_comp_chir.comp_id
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_chem_comp_chir.id
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_chem_comp_chir.atom_id_centre
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_chem_comp_chir.atom_id_1
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_chem_comp_chir.atom_id_2
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_chem_comp_chir.atom_id_3
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_chem_comp_chir.volume_sign
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TYR chir_1 CA N C CB positive
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loop_
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_chem_comp_plane_atom.comp_id
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_chem_comp_plane_atom.plane_id
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_chem_comp_plane_atom.atom_id
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_chem_comp_plane_atom.dist_esd
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TYR plan-1 CB 0.020
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TYR plan-1 CD1 0.020
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TYR plan-1 CD2 0.020
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TYR plan-1 CE1 0.020
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TYR plan-1 CE2 0.020
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TYR plan-1 CG 0.020
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TYR plan-1 CZ 0.020
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TYR plan-1 HD1 0.020
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TYR plan-1 HD2 0.020
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TYR plan-1 HE1 0.020
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TYR plan-1 HE2 0.020
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TYR plan-1 OH 0.020
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TYR plan-2 C 0.020
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TYR plan-2 CA 0.020
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TYR plan-2 O 0.020
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TYR plan-2 OXT 0.020
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loop_
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_pdbx_chem_comp_descriptor.comp_id
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_pdbx_chem_comp_descriptor.type
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_pdbx_chem_comp_descriptor.program
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_pdbx_chem_comp_descriptor.program_version
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_pdbx_chem_comp_descriptor.descriptor
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TYR SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1ccc(O)cc1"
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TYR SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1ccc(O)cc1)C(O)=O"
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TYR SMILES CACTVS 3.341 "N[CH](Cc1ccc(O)cc1)C(O)=O"
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TYR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1C[C@@H](C(=O)O)N)O"
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TYR SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CC(C(=O)O)N)O"
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TYR InChI InChI 1.03 "InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/t8-/m0/s1"
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TYR InChIKey InChI 1.03 OUYCCCASQSFEME-QMMMGPOBSA-N
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loop_
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_pdbx_chem_comp_description_generator.comp_id
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_pdbx_chem_comp_description_generator.program_name
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_pdbx_chem_comp_description_generator.program_version
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_pdbx_chem_comp_description_generator.descriptor
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TYR acedrg 278 "dictionary generator"
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TYR acedrg_database 12 "data source"
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TYR rdkit 2019.09.1 "Chemoinformatics tool"
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TYR refmac5 5.8.0419 "optimization tool"
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TYR servalcat 0.4.57 'optimization tool'
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