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>
222 lines
5.7 KiB
Plaintext
222 lines
5.7 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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VAL VAL VALINE peptide 19 8 .
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data_comp_VAL
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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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VAL N N NT3 1 11.307 2.990 48.522
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VAL CA C CH1 0 10.346 4.137 48.590
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VAL C C C 0 9.715 4.163 49.994
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VAL O O O 0 9.179 3.107 50.398
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VAL CB C CH1 0 9.259 4.073 47.494
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VAL CG1 C CH3 0 8.396 5.334 47.475
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VAL CG2 C CH3 0 9.849 3.802 46.112
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VAL OXT O OC -1 9.782 5.237 50.630
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VAL H H H 0 11.930 3.145 47.888
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VAL H2 H H 0 10.867 2.229 48.319
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VAL H3 H H 0 11.735 2.877 49.308
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VAL HA H H 0 10.853 4.963 48.468
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VAL HB H H 0 8.670 3.315 47.717
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VAL HG11 H H 0 8.964 6.117 47.567
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VAL HG12 H H 0 7.763 5.306 48.212
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VAL HG13 H H 0 7.907 5.387 46.637
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VAL HG21 H H 0 10.555 4.444 45.928
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VAL HG22 H H 0 9.155 3.884 45.436
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VAL HG23 H H 0 10.217 2.902 46.084
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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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VAL N n/a CA START
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VAL H N . .
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VAL H2 N . .
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VAL H3 N . .
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VAL CA N C .
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VAL HA CA . .
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VAL CB CA CG2 .
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VAL HB CB . .
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VAL CG1 CB HG13 .
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VAL HG11 CG1 . .
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VAL HG12 CG1 . .
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VAL HG13 CG1 . .
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VAL CG2 CB HG23 .
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VAL HG21 CG2 . .
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VAL HG22 CG2 . .
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VAL HG23 CG2 . .
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VAL C CA . END
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VAL O C . .
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VAL OXT C . .
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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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VAL N N(CCCH)(H)3
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VAL CA C(CCCH)(NH3)(COO)(H)
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VAL C C(CCHN)(O)2
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VAL O O(CCO)
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VAL CB C(CCHN)(CH3)2(H)
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VAL CG1 C(CCCH)(H)3
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VAL CG2 C(CCCH)(H)3
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VAL OXT O(CCO)
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VAL H H(NCHH)
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VAL H2 H(NCHH)
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VAL H3 H(NCHH)
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VAL HA H(CCCN)
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VAL HB H(CC3)
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VAL HG11 H(CCHH)
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VAL HG12 H(CCHH)
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VAL HG13 H(CCHH)
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VAL HG21 H(CCHH)
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VAL HG22 H(CCHH)
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VAL HG23 H(CCHH)
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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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VAL N CA SINGLE n 1.495 0.0100 1.495 0.0100
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VAL CA C SINGLE n 1.538 0.0100 1.538 0.0100
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VAL CA CB SINGLE n 1.541 0.0101 1.541 0.0101
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VAL C O DOUBLE n 1.251 0.0183 1.251 0.0183
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VAL C OXT SINGLE n 1.251 0.0183 1.251 0.0183
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VAL CB CG1 SINGLE n 1.524 0.0131 1.524 0.0131
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VAL CB CG2 SINGLE n 1.524 0.0131 1.524 0.0131
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VAL N H SINGLE n 1.018 0.0520 0.902 0.0102
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VAL N H2 SINGLE n 1.018 0.0520 0.902 0.0102
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VAL N H3 SINGLE n 1.018 0.0520 0.902 0.0102
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VAL CA HA SINGLE n 1.092 0.0100 0.977 0.0200
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VAL CB HB SINGLE n 1.092 0.0100 0.986 0.0184
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VAL CG1 HG11 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG1 HG12 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG1 HG13 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156
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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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VAL CA N H 109.990 2.80
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VAL CA N H2 109.990 2.80
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VAL CA N H3 109.990 2.80
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VAL H N H2 109.032 3.00
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VAL H N H3 109.032 3.00
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VAL H2 N H3 109.032 3.00
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VAL N CA C 108.738 1.50
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VAL N CA CB 111.627 2.88
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VAL N CA HA 108.328 1.50
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VAL C CA CB 111.231 1.50
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VAL C CA HA 108.550 1.50
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VAL CB CA HA 108.536 1.50
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VAL CA C O 117.155 1.50
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VAL CA C OXT 117.155 1.50
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VAL O C OXT 125.690 1.50
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VAL CA CB CG1 111.834 1.50
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VAL CA CB CG2 111.834 1.50
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VAL CA CB HB 107.069 1.50
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VAL CG1 CB CG2 110.700 1.76
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VAL CG1 CB HB 107.681 2.06
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VAL CG2 CB HB 107.681 2.06
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VAL CB CG1 HG11 109.510 1.50
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VAL CB CG1 HG12 109.510 1.50
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VAL CB CG1 HG13 109.510 1.50
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VAL HG11 CG1 HG12 109.390 1.50
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VAL HG11 CG1 HG13 109.390 1.50
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VAL HG12 CG1 HG13 109.390 1.50
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VAL CB CG2 HG21 109.510 1.50
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VAL CB CG2 HG22 109.510 1.50
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VAL CB CG2 HG23 109.510 1.50
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VAL HG21 CG2 HG22 109.390 1.50
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VAL HG21 CG2 HG23 109.390 1.50
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VAL HG22 CG2 HG23 109.390 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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VAL chi1 N CA CB CG2 -60.000 10.0 3
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VAL hh1 CA CB CG1 HG13 180.000 10.0 3
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VAL hh2 CA CB CG2 HG23 -60.000 10.0 3
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VAL sp3_sp3_1 C CA N H 180.000 10.0 3
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VAL 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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VAL chir_1 CA N C CB positive
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VAL chir_2 CB CA CG1 CG2 both
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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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VAL plan-1 C 0.020
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VAL plan-1 CA 0.020
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VAL plan-1 O 0.020
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VAL 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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VAL SMILES ACDLabs 10.04 O=C(O)C(N)C(C)C
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VAL SMILES_CANONICAL CACTVS 3.341 CC(C)[C@H](N)C(O)=O
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VAL SMILES CACTVS 3.341 CC(C)[CH](N)C(O)=O
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VAL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)[C@@H](C(=O)O)N
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VAL SMILES "OpenEye OEToolkits" 1.5.0 CC(C)C(C(=O)O)N
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VAL InChI InChI 1.03 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1
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VAL InChIKey InChI 1.03 KZSNJWFQEVHDMF-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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VAL acedrg 278 "dictionary generator"
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VAL acedrg_database 12 "data source"
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VAL rdkit 2019.09.1 "Chemoinformatics tool"
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VAL refmac5 5.8.0419 "optimization tool"
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