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>
199 lines
5.1 KiB
Plaintext
199 lines
5.1 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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ASP ASP "ASPARTIC ACID" peptide 15 9 .
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data_comp_ASP
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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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ASP N N NT3 1 33.542 17.835 39.145
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ASP CA C CH1 0 34.991 17.614 38.867
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ASP C C C 0 35.178 17.161 37.413
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ASP O O O 0 36.268 17.442 36.867
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ASP CB C CH2 0 35.617 16.650 39.866
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ASP CG C C 0 34.932 15.299 40.037
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ASP OD1 O O 0 35.515 14.435 40.725
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ASP OD2 O OC -1 33.817 15.122 39.501
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ASP OXT O OC -1 34.232 16.542 36.875
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ASP H H H 0 33.408 17.940 40.031
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ASP H2 H H 0 33.045 17.139 38.857
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ASP H3 H H 0 33.263 18.581 38.722
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ASP HA H H 0 35.453 18.476 38.978
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ASP HB3 H H 0 35.641 17.087 40.742
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ASP HB2 H H 0 36.543 16.483 39.592
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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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ASP N n/a CA START
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ASP H N . .
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ASP H2 N . .
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ASP H3 N . .
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ASP CA N C .
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ASP HA CA . .
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ASP CB CA CG .
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ASP HB3 CB . .
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ASP HB2 CB . .
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ASP CG CB OD2 .
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ASP OD1 CG . .
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ASP OD2 CG . .
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ASP C CA . END
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ASP O C . .
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ASP 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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ASP N N(CCCH)(H)3
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ASP CA C(CCHH)(NH3)(COO)(H)
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ASP C C(CCHN)(O)2
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ASP O O(CCO)
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ASP CB C(CCHN)(COO)(H)2
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ASP CG C(CCHH)(O)2
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ASP OD1 O(CCO)
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ASP OD2 O(CCO)
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ASP OXT O(CCO)
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ASP H H(NCHH)
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ASP H2 H(NCHH)
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ASP H3 H(NCHH)
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ASP HA H(CCCN)
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ASP HB3 H(CCCH)
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ASP HB2 H(CCCH)
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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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ASP N CA SINGLE n 1.490 0.0100 1.490 0.0100
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ASP CA C SINGLE n 1.533 0.0100 1.533 0.0100
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ASP CA CB SINGLE n 1.521 0.0100 1.521 0.0100
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ASP C O DOUBLE n 1.251 0.0183 1.251 0.0183
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ASP C OXT SINGLE n 1.251 0.0183 1.251 0.0183
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ASP CB CG SINGLE n 1.522 0.0100 1.522 0.0100
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ASP CG OD1 DOUBLE n 1.249 0.0161 1.249 0.0161
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ASP CG OD2 SINGLE n 1.249 0.0161 1.249 0.0161
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ASP N H SINGLE n 1.018 0.0520 0.902 0.0102
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ASP N H2 SINGLE n 1.018 0.0520 0.902 0.0102
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ASP N H3 SINGLE n 1.018 0.0520 0.902 0.0102
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ASP CA HA SINGLE n 1.092 0.0100 0.984 0.0200
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ASP CB HB3 SINGLE n 1.092 0.0100 0.980 0.0165
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ASP CB HB2 SINGLE n 1.092 0.0100 0.980 0.0165
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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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ASP CA N H 109.990 3.00
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ASP CA N H2 109.990 3.00
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ASP CA N H3 109.990 3.00
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ASP H N H2 109.032 3.00
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ASP H N H3 109.032 3.00
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ASP H2 N H3 109.032 3.00
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ASP N CA C 109.258 1.50
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ASP N CA CB 111.400 1.50
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ASP N CA HA 108.387 1.58
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ASP C CA CB 112.421 3.00
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ASP C CA HA 108.774 1.79
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ASP CB CA HA 108.472 2.65
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ASP CA C O 117.148 1.60
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ASP CA C OXT 117.148 1.60
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ASP O C OXT 125.704 1.50
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ASP CA CB CG 115.436 1.50
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ASP CA CB HB3 108.799 3.00
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ASP CA CB HB2 108.799 3.00
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ASP CG CB HB3 108.242 2.79
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ASP CG CB HB2 108.242 2.79
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ASP HB3 CB HB2 107.976 2.66
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ASP CB CG OD1 117.985 1.50
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ASP CB CG OD2 117.985 1.50
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ASP OD1 CG OD2 124.031 1.82
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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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ASP chi1 N CA CB CG -60.000 10.0 3
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ASP chi2 CA CB CG OD1 180.000 10.0 6
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ASP sp3_sp3_1 C CA N H 180.000 10.0 3
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ASP 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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ASP 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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ASP plan-1 C 0.020
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ASP plan-1 CA 0.020
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ASP plan-1 O 0.020
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ASP plan-1 OXT 0.020
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ASP plan-2 CB 0.020
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ASP plan-2 CG 0.020
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ASP plan-2 OD1 0.020
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ASP plan-2 OD2 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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ASP SMILES ACDLabs 12.01 O=C(O)CC(N)C(=O)O
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ASP SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC(O)=O)C(O)=O
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ASP SMILES CACTVS 3.370 N[CH](CC(O)=O)C(O)=O
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ASP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C([C@@H](C(=O)O)N)C(=O)O
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ASP SMILES "OpenEye OEToolkits" 1.7.0 C(C(C(=O)O)N)C(=O)O
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ASP InChI InChI 1.03 InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1
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ASP InChIKey InChI 1.03 CKLJMWTZIZZHCS-REOHCLBHSA-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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ASP acedrg 278 "dictionary generator"
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ASP acedrg_database 12 "data source"
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ASP rdkit 2019.09.1 "Chemoinformatics tool"
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ASP refmac5 5.8.0419 "optimization tool"
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