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>
118 lines
5.1 KiB
Plaintext
118 lines
5.1 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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DMS DMS "DIMETHYL SULFOXIDE" NON-POLYMER 10 4 .
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#
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data_comp_DMS
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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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DMS S S S3 0 63.218 46.394 -11.587
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DMS O O O 0 63.732 46.133 -12.975
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DMS C1 C CH3 0 64.619 46.928 -10.638
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DMS C2 C CH3 0 63.010 44.801 -10.834
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DMS H11 H H 0 64.347 47.082 -9.723
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DMS H12 H H 0 64.967 47.748 -11.014
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DMS H13 H H 0 65.302 46.245 -10.662
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DMS H21 H H 0 63.858 44.337 -10.825
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DMS H22 H H 0 62.366 44.288 -11.340
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DMS H23 H H 0 62.693 44.913 -9.927
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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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DMS S O DOUBLE n 1.503 0.0200 1.503 0.0200
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DMS S C1 SINGLE n 1.774 0.0176 1.774 0.0176
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DMS S C2 SINGLE n 1.774 0.0176 1.774 0.0176
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DMS C1 H11 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C1 H12 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C1 H13 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C2 H21 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C2 H22 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C2 H23 SINGLE n 1.089 0.0100 0.967 0.0136
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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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DMS O S C1 106.047 1.50
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DMS O S C2 106.047 1.50
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DMS C1 S C2 97.789 1.50
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DMS S C1 H11 109.408 1.50
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DMS S C1 H12 109.408 1.50
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DMS S C1 H13 109.408 1.50
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DMS H11 C1 H12 109.545 1.50
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DMS H11 C1 H13 109.545 1.50
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DMS H12 C1 H13 109.545 1.50
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DMS S C2 H21 109.408 1.50
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DMS S C2 H22 109.408 1.50
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DMS S C2 H23 109.408 1.50
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DMS H21 C2 H22 109.545 1.50
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DMS H21 C2 H23 109.545 1.50
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DMS H22 C2 H23 109.545 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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DMS sp3_sp3_1 H11 C1 S O 180.000 10.0 3
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DMS sp3_sp3_8 H21 C2 S O -60.000 10.0 3
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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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DMS chir_1 S O C1 C2 both
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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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DMS SMILES ACDLabs 10.04 sulfinyldimethane
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DMS SMILES_CANONICAL CACTVS 3.341 C[S](C)=O
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DMS SMILES CACTVS 3.341 C[S](C)=O
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DMS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CS(=O)C
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DMS SMILES "OpenEye OEToolkits" 1.5.0 CS(=O)C
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DMS InChI InChI 1.03 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
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DMS InChIKey InChI 1.03 IAZDPXIOMUYVGZ-UHFFFAOYSA-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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DMS acedrg 243 "dictionary generator"
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DMS acedrg_database 11 "data source"
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DMS rdkit 2017.03.2 "Chemoinformatics tool"
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DMS refmac5 5.8.0238 "optimization tool"
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