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>
217 lines
6.3 KiB
Plaintext
217 lines
6.3 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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PRO PRO PROLINE P-peptide 17 8 .
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data_comp_PRO
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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.alt_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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PRO N N N NT2 1 39.160 37.649 83.026
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PRO CA CA C CH1 0 38.550 38.680 82.125
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PRO C C C C 0 37.155 39.077 82.602
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PRO O O O O 0 36.450 38.196 83.146
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PRO CB CB C CH2 0 38.553 38.007 80.756
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PRO CG CG C CH2 0 38.265 36.558 81.098
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PRO CD CD C CH2 0 38.934 36.298 82.416
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PRO OXT OXT O OC -1 36.821 40.268 82.409
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PRO H H H H 0 40.054 37.806 83.097
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PRO H2 H2 H H 0 38.800 37.681 83.862
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PRO HA HA H H 0 39.125 39.473 82.102
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PRO HB3 HB3 H H 0 39.422 38.100 80.320
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PRO HB2 HB2 H H 0 37.858 38.378 80.178
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PRO HG3 HG3 H H 0 38.625 35.964 80.410
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PRO HG2 HG2 H H 0 37.302 36.406 81.169
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PRO HD3 HD3 H H 0 38.363 35.755 82.994
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PRO HD2 HD2 H H 0 39.785 35.835 82.289
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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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PRO N n/a CA START
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PRO CA N C .
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PRO HA CA . .
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PRO CB CA CG .
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PRO HB3 CB . .
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PRO HB2 CB . .
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PRO CG CB CD .
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PRO HG3 CG . .
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PRO HG2 CG . .
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PRO CD CG HD2 .
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PRO HD3 CD . .
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PRO HD2 CD . .
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PRO C CA . END
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PRO O C . .
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PRO OXT C . .
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PRO H N . .
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PRO H2 N . .
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PRO CD N . 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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PRO N N[5](C[5]C[5]CH)(C[5]C[5]HH)(H)2{4|H<1>}
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PRO CA C[5](C[5]C[5]HH)(N[5]C[5]HH)(COO)(H){4|H<1>}
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PRO C C(C[5]C[5]N[5]H)(O)2
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PRO O O(CC[5]O)
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PRO CB C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{4|H<1>}
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PRO CG C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,3|H<1>}
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PRO CD C[5](C[5]C[5]HH)(N[5]C[5]HH)(H)2{1|C<3>,3|H<1>}
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PRO OXT O(CC[5]O)
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PRO H H(N[5]C[5]2H)
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PRO H2 H(N[5]C[5]2H)
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PRO HA H(C[5]C[5]N[5]C)
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PRO HB3 H(C[5]C[5]2H)
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PRO HB2 H(C[5]C[5]2H)
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PRO HG3 H(C[5]C[5]2H)
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PRO HG2 H(C[5]C[5]2H)
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PRO HD3 H(C[5]C[5]N[5]H)
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PRO HD2 H(C[5]C[5]N[5]H)
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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.value_order
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_chem_comp_bond.pdbx_aromatic_flag
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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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PRO N CA SINGLE n 1.496 0.0142 1.496 0.0142
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PRO N CD SINGLE n 1.499 0.0135 1.499 0.0135
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PRO CA C SINGLE n 1.525 0.0103 1.525 0.0103
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PRO CA CB SINGLE n 1.526 0.0157 1.526 0.0157
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PRO C O DOUBLE n 1.252 0.0117 1.252 0.0117
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PRO C OXT SINGLE n 1.252 0.0117 1.252 0.0117
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PRO CB CG SINGLE n 1.516 0.0179 1.516 0.0179
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PRO CG CD SINGLE n 1.497 0.0200 1.497 0.0200
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PRO N H SINGLE n 1.018 0.0520 0.910 0.0200
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PRO N H2 SINGLE n 1.018 0.0520 0.910 0.0200
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PRO CA HA SINGLE n 1.092 0.0100 0.980 0.0200
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PRO CB HB3 SINGLE n 1.092 0.0100 0.977 0.0145
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PRO CB HB2 SINGLE n 1.092 0.0100 0.977 0.0145
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PRO CG HG3 SINGLE n 1.092 0.0100 0.978 0.0181
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PRO CG HG2 SINGLE n 1.092 0.0100 0.978 0.0181
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PRO CD HD3 SINGLE n 1.092 0.0100 0.977 0.0199
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PRO CD HD2 SINGLE n 1.092 0.0100 0.977 0.0199
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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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PRO CA N CD 107.978 1.50
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PRO CA N H 109.889 3.00
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PRO CA N H2 109.889 3.00
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PRO CD N H 110.257 3.00
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PRO CD N H2 110.257 3.00
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PRO H N H2 108.772 3.00
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PRO N CA C 110.397 1.50
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PRO N CA CB 103.994 1.50
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PRO N CA HA 109.579 1.50
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PRO C CA CB 113.159 3.00
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PRO C CA HA 109.687 1.50
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PRO CB CA HA 109.910 1.89
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PRO CA C O 116.979 3.00
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PRO CA C OXT 116.979 3.00
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PRO O C OXT 126.043 1.52
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PRO CA CB CG 101.701 3.00
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PRO CA CB HB3 110.865 1.50
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PRO CA CB HB2 110.865 1.50
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PRO CG CB HB3 110.891 1.59
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PRO CG CB HB2 110.891 1.59
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PRO HB3 CB HB2 108.880 2.25
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PRO CB CG CD 105.541 3.00
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PRO CB CG HG3 110.897 1.50
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PRO CB CG HG2 110.897 1.50
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PRO CD CG HG3 110.621 1.50
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PRO CD CG HG2 110.621 1.50
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PRO HG3 CG HG2 108.871 1.50
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PRO N CD CG 104.386 2.30
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PRO N CD HD3 110.569 1.50
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PRO N CD HD2 110.569 1.50
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PRO CG CD HD3 111.131 1.62
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PRO CG CD HD2 111.131 1.62
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PRO HD3 CD HD2 109.116 1.50
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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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PRO chi1 N CA CB CG -60.000 10.0 3
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PRO chi2 CA CB CG CD 180.000 10.0 3
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PRO sp3_sp3_1 CB CA N CD 60.000 10.0 3
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PRO sp3_sp3_28 N CD CG CB -60.000 10.0 3
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PRO sp3_sp3_37 CG CD N CA 180.000 10.0 3
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PRO 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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PRO 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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PRO plan-1 C 0.020
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PRO plan-1 CA 0.020
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PRO plan-1 O 0.020
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PRO plan-1 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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PRO SMILES ACDLabs 10.04 "O=C(O)C1NCCC1"
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PRO SMILES_CANONICAL CACTVS 3.341 "OC(=O)[C@@H]1CCCN1"
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PRO SMILES CACTVS 3.341 "OC(=O)[CH]1CCCN1"
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PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@H](NC1)C(=O)O"
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PRO SMILES "OpenEye OEToolkits" 1.5.0 "C1CC(NC1)C(=O)O"
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PRO InChI InChI 1.03 "InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"
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PRO InChIKey InChI 1.03 ONIBWKKTOPOVIA-BYPYZUCNSA-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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PRO acedrg 281 "dictionary generator"
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PRO acedrg_database 12 "data source"
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PRO rdkit 2019.09.1 "Chemoinformatics tool"
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PRO refmac5 5.8.0419 "optimization tool"
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