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>
105 lines
4.3 KiB
Plaintext
105 lines
4.3 KiB
Plaintext
#
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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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ACT ACT "ACETATE ION" NON-POLYMER 7 4 .
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#
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data_comp_ACT
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#
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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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ACT C C C 0 50.652 -7.080 41.537
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ACT O O O 0 50.915 -7.323 42.732
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ACT OXT O OC -1 51.516 -6.945 40.648
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ACT CH3 C CH3 0 49.181 -6.939 41.139
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ACT H1 H H 0 49.117 -6.760 40.187
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ACT H2 H H 0 48.780 -6.205 41.632
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ACT H3 H H 0 48.708 -7.761 41.345
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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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ACT C O DOUBLE n 1.247 0.0187 1.247 0.0187
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ACT C OXT SINGLE n 1.247 0.0187 1.247 0.0187
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ACT C CH3 SINGLE n 1.530 0.0200 1.530 0.0200
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ACT CH3 H1 SINGLE n 1.089 0.0100 0.971 0.0140
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ACT CH3 H2 SINGLE n 1.089 0.0100 0.971 0.0140
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ACT CH3 H3 SINGLE n 1.089 0.0100 0.971 0.0140
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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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ACT O C OXT 123.884 1.50
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ACT O C CH3 118.052 1.94
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ACT OXT C CH3 118.052 1.94
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ACT C CH3 H1 109.670 1.50
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ACT C CH3 H2 109.670 1.50
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ACT C CH3 H3 109.670 1.50
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ACT H1 CH3 H2 109.424 1.50
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ACT H1 CH3 H3 109.424 1.50
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ACT H2 CH3 H3 109.424 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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ACT sp2_sp3_1 O C CH3 H1 0.000 10.0 6
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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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ACT plan-1 C 0.020
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ACT plan-1 CH3 0.020
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ACT plan-1 O 0.020
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ACT 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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ACT SMILES ACDLabs 10.04 "[O-]C(=O)C"
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ACT SMILES_CANONICAL CACTVS 3.341 CC([O-])=O
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ACT SMILES CACTVS 3.341 CC([O-])=O
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ACT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=O)[O-]
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ACT SMILES "OpenEye OEToolkits" 1.5.0 CC(=O)[O-]
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ACT InChI InChI 1.03 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
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ACT InChIKey InChI 1.03 QTBSBXVTEAMEQO-UHFFFAOYSA-M
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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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ACT acedrg 243 "dictionary generator"
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ACT acedrg_database 11 "data source"
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ACT rdkit 2017.03.2 "Chemoinformatics tool"
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ACT refmac5 5.8.0238 "optimization tool"
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