From 70102327cef2acad338331869625d42e1b5277c3 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Mon, 16 Sep 2024 14:37:35 +0200 Subject: [PATCH 1/4] Sync catalogs --- app/catalogs/haddock3.easy.json | 232 ++++-- app/catalogs/haddock3.expert.json | 1094 ++++++---------------------- app/catalogs/haddock3.guru.json | 1124 +++++++---------------------- 3 files changed, 661 insertions(+), 1789 deletions(-) diff --git a/app/catalogs/haddock3.easy.json b/app/catalogs/haddock3.easy.json index 980f7782..95847d2e 100644 --- a/app/catalogs/haddock3.easy.json +++ b/app/catalogs/haddock3.easy.json @@ -363,6 +363,13 @@ "$comment": "Evaluate DockQ. A single continuous quality measure for protein docked models based on the CAPRI criteria, a combination of i-RMSD, l-RMSD and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879`", "type": "boolean" }, + "global_rmsd": { + "default": true, + "title": "Calculate global RMSD", + "description": "Calculate full structure RMSD.", + "$comment": "Compute full structure RMSD between reference structure and the model after superimposition. Note that a sequence alignment is performed to obtain the mapping between the reference and the model. If the one of the structure contain a 'small-molecule', we assume that the compared structure atoms are in the same order. With default parameters `allatoms = false`, only backbone RMSD will be computed.", + "type": "boolean" + }, "irmsd_cutoff": { "default": 10, "title": "Distance cutoff (Å) used to define interface residues.", @@ -392,7 +399,7 @@ "format": "chain" }, "ligand_chains": { - "default": ["B"], + "default": [], "title": "Ligand ChainIDs", "description": "Ligand ChainIDs to be considered for the RMSD calculations.", "$comment": "Ligand ChainIDs to be considered for the RMSD calculations. This determines which chains will be treated as the ligand for the L-RMSD and for I-L-RMSD.", @@ -479,6 +486,9 @@ "dockq": { "ui:group": "analysis" }, + "global_rmsd": { + "ui:group": "analysis" + }, "irmsd_cutoff": { "ui:group": "analysis" }, @@ -785,6 +795,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -835,10 +846,9 @@ "$comment": "Force constant applied to the dihedral angle restraints read from dihe_fname.", "type": "number", "maximum": 9999, - "minimum": -9999 + "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -853,8 +863,8 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 9999, - "minimum": -9999 + "maximum": 180, + "minimum": 0 }, "dnarest_on": { "default": false, @@ -863,6 +873,20 @@ "$comment": "This option allows to restraint the conformation of nucleic acids based on the values from the input structures. The following restraints will be automatically defined: - single base planarity - sugar pucker - phosphate backbone diherdral angle restraints - Watson-Crick base pairing", "type": "boolean" }, + "ligand_param_fname": { + "title": "Custom ligand parameter file", + "description": "Ligand parameter file in CNS format", + "$comment": "Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, + "ligand_top_fname": { + "title": "Custom ligand topology file", + "description": "Ligand topology file in CNS format", + "$comment": "Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, "elecflag": { "default": true, "title": "Include electrostatics energy", @@ -910,6 +934,14 @@ "dnarest_on": { "ui:group": "other restraints" }, + "ligand_param_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, + "ligand_top_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, "elecflag": { "ui:group": "force field" } @@ -928,6 +960,20 @@ "schema": { "type": "object", "properties": { + "ligand_param_fname": { + "title": "Custom ligand parameter file", + "description": "Ligand parameter file in CNS format", + "$comment": "Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, + "ligand_top_fname": { + "title": "Custom ligand topology file", + "description": "Ligand topology file in CNS format", + "$comment": "Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, "elecflag": { "default": true, "title": "Include electrostatics energy", @@ -940,6 +986,14 @@ "additionalProperties": false }, "uiSchema": { + "ligand_param_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, + "ligand_top_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, "elecflag": { "ui:group": "force field" } @@ -957,6 +1011,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -1001,7 +1056,6 @@ "type": "boolean" }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -1016,8 +1070,8 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 9999, - "minimum": -9999 + "maximum": 180, + "minimum": 0 }, "dnarest_on": { "default": false, @@ -1026,6 +1080,20 @@ "$comment": "This option allows to restraint the conformation of nucleic acids based on the values from the input structures. The following restraints will be automatically defined: - single base planarity - sugar pucker - phosphate backbone diherdral angle restraints - Watson-Crick base pairing", "type": "boolean" }, + "ligand_param_fname": { + "title": "Custom ligand parameter file", + "description": "Ligand parameter file in CNS format", + "$comment": "Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, + "ligand_top_fname": { + "title": "Custom ligand topology file", + "description": "Ligand topology file in CNS format", + "$comment": "Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, "elecflag": { "default": true, "title": "Include electrostatics energy", @@ -1079,6 +1147,14 @@ "dnarest_on": { "ui:group": "other restraints" }, + "ligand_param_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, + "ligand_top_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, "elecflag": { "ui:group": "force field" }, @@ -1135,10 +1211,10 @@ "format": "chain" }, "ligand_chains": { - "default": ["B"], + "default": [], "title": "Ligand ChainIDs", "description": "Ligand ChainIDs to be considered for the IL-RMSD calculations.", - "$comment": "Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be treated as the ligand for the IL-RMSD.", + "$comment": "Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be treated as the ligand for the IL-RMSD. By default, all chains are considered with the exception of the receptor chain.", "type": "array", "minItems": 0, "maxItems": 100, @@ -1340,6 +1416,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -1383,8 +1460,16 @@ "$comment": "Turns on dihedral angle restraints. Those should be defined in the dihe_fname file.", "type": "boolean" }, + "dihedrals_scale": { + "default": 200, + "title": "Force constant for dihedral angle restraints", + "description": "Force constant applied to the dihedral angle restraints read from dihe_fname.", + "$comment": "Force constant applied to the dihedral angle restraints read from dihe_fname.", + "type": "number", + "maximum": 9999, + "minimum": 0 + }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -1399,7 +1484,7 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 1000, + "maximum": 180, "minimum": 0 }, "dnarest_on": { @@ -1409,6 +1494,20 @@ "$comment": "This option allows to restraint the conformation of nucleic acids based on the values from the input structures. The following restraints will be automatically defined: - single base planarity - sugar pucker - phosphate backbone diherdral angle restraints - Watson-Crick base pairing", "type": "boolean" }, + "ligand_param_fname": { + "title": "Custom ligand parameter file", + "description": "Ligand parameter file in CNS format", + "$comment": "Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, + "ligand_top_fname": { + "title": "Custom ligand topology file", + "description": "Ligand topology file in CNS format", + "$comment": "Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, "elecflag": { "default": true, "title": "Include electrostatics energy", @@ -1454,6 +1553,9 @@ "dihedrals_on": { "ui:group": "dihedral restraints" }, + "dihedrals_scale": { + "ui:group": "dihedral restraints" + }, "ssdihed": { "ui:group": "dihedral restraints" }, @@ -1463,6 +1565,14 @@ "dnarest_on": { "ui:group": "other restraints" }, + "ligand_param_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, + "ligand_top_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, "elecflag": { "ui:group": "force field" } @@ -1482,7 +1592,6 @@ "type": "object", "properties": { "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -1507,6 +1616,20 @@ "$comment": "This option allows to restraint the conformation of nucleic acids based on the values from the input structures. The following restraints will be automatically defined: - single base planarity - sugar pucker - phosphate backbone diherdral angle restraints - Watson-Crick base pairing", "type": "boolean" }, + "ligand_param_fname": { + "title": "Custom ligand parameter file", + "description": "Ligand parameter file in CNS format", + "$comment": "Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, + "ligand_top_fname": { + "title": "Custom ligand topology file", + "description": "Ligand topology file in CNS format", + "$comment": "Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, "elecflag": { "default": true, "title": "Include electrostatics energy", @@ -1538,6 +1661,14 @@ "dnarest_on": { "ui:group": "other restraints" }, + "ligand_param_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, + "ligand_top_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, "elecflag": { "ui:group": "force field" } @@ -1555,6 +1686,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -1816,6 +1948,20 @@ "$comment": "Since HADDOCK uses a united atom force field, the non-polar hydrogen atoms can be in principle discarded. This saves computing time. However this should not be done if you are defining distance restraints to specific hydrogen atoms (e.g. when using NMR distance restraints).", "type": "boolean" }, + "ligand_param_fname": { + "title": "Custom ligand parameter file", + "description": "Ligand parameter file in CNS format", + "$comment": "Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, + "ligand_top_fname": { + "title": "Custom ligand topology file", + "description": "Ligand topology file in CNS format", + "$comment": "Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions...) for any ligand not supported by default by HADDOCK", + "type": "string", + "format": "uri-reference" + }, "mol": { "title": "Input molecule configuration", "$comment": "You can expand this parameter and associated sub-parameters to the other input molecules. For example, if you input three molecules, you can define mol1, mol2, and mol3 subparameters. Those not defined will be populated with the defaults.", @@ -1829,48 +1975,6 @@ "description": "Defines the molecule as a cyclic peptide", "$comment": "This option defines the molecule as a cyclic peptide and HADDOCK will generate a peptide bond between the N- and C-ter provided those are within 2A. This cutoff can be changed in the generate-topology.cns script.", "type": "boolean" - }, - "nhisd": { - "default": 0, - "title": "Number of HISD residue", - "description": "Defines the number of HISD residues (neutral HIS with the proton on the ND atom) residues when autohis=false", - "$comment": "Defines the number of HISD residues (neutral HIS with the proton on the ND atom) residues. The corresponding residue numbers must be defined in the following parameter (hisd_1, hisd_2, ...). Add as many as needed. Note that HIS is interpreted as a charged Histidine)", - "type": "number", - "maximum": 9999, - "minimum": 0 - }, - "hisd": { - "type": "array", - "items": { - "title": "HISD residue number", - "description": "Residue number of the Histidine to be defined as HISD", - "$comment": "Residue number of the Histidine to be defined as HISD", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } - }, - "nhise": { - "default": 0, - "title": "Number of HISE residue", - "description": "Defines the number of HISE residues (neutral HIS with the proton on the NE atom) residues when autohis=false", - "$comment": "Defines the number of HISE residues (neutral HIS with the proton on the NE atom) residues. The corresponding residue numbers must be defined in the following parameter (hise_1, hise_2, ...). Add as many as needed. Note that HIS is interpreted as a charged Histidine)", - "type": "number", - "maximum": 9999, - "minimum": 0 - }, - "hise": { - "type": "array", - "items": { - "title": "HISE residue number", - "description": "Residue number of the Histidine to be defined as HISE", - "$comment": "Residue number of the Histidine to be defined as HISE", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } } }, "required": [], @@ -1886,6 +1990,14 @@ "delenph": { "ui:group": "molecule" }, + "ligand_param_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, + "ligand_top_fname": { + "ui:widget": "file", + "ui:group": "force field" + }, "mol": { "ui:indexable": true, "ui:group": "input molecules" @@ -1895,15 +2007,7 @@ "mol": { "indexed": true, "items": { - "sectioned": true, - "properties": { - "hisd": { - "indexed": true - }, - "hise": { - "indexed": true - } - } + "sectioned": true } } } diff --git a/app/catalogs/haddock3.expert.json b/app/catalogs/haddock3.expert.json index aeed9481..f86b5f9c 100644 --- a/app/catalogs/haddock3.expert.json +++ b/app/catalogs/haddock3.expert.json @@ -403,6 +403,13 @@ "$comment": "Evaluate DockQ. A single continuous quality measure for protein docked models based on the CAPRI criteria, a combination of i-RMSD, l-RMSD and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879`", "type": "boolean" }, + "global_rmsd": { + "default": true, + "title": "Calculate global RMSD", + "description": "Calculate full structure RMSD.", + "$comment": "Compute full structure RMSD between reference structure and the model after superimposition. Note that a sequence alignment is performed to obtain the mapping between the reference and the model. If the one of the structure contain a 'small-molecule', we assume that the compared structure atoms are in the same order. With default parameters `allatoms = false`, only backbone RMSD will be computed.", + "type": "boolean" + }, "irmsd_cutoff": { "default": 10, "title": "Distance cutoff (Å) used to define interface residues.", @@ -432,7 +439,7 @@ "format": "chain" }, "ligand_chains": { - "default": ["B"], + "default": [], "title": "Ligand ChainIDs", "description": "Ligand ChainIDs to be considered for the RMSD calculations.", "$comment": "Ligand ChainIDs to be considered for the RMSD calculations. This determines which chains will be treated as the ligand for the L-RMSD and for I-L-RMSD.", @@ -519,6 +526,9 @@ "dockq": { "ui:group": "analysis" }, + "global_rmsd": { + "ui:group": "analysis" + }, "irmsd_cutoff": { "ui:group": "analysis" }, @@ -882,6 +892,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -893,6 +904,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -929,7 +941,7 @@ "type": "string", "format": "uri-reference" }, - "amb_scale": { + "ambig_scale": { "default": 50, "title": "Force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname.", @@ -938,7 +950,7 @@ "maximum": 1000, "minimum": 0 }, - "unamb_scale": { + "unambig_scale": { "default": 50, "title": "Force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname.", @@ -1009,10 +1021,9 @@ "$comment": "Force constant applied to the dihedral angle restraints read from dihe_fname.", "type": "number", "maximum": 9999, - "minimum": -9999 + "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -1027,8 +1038,8 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 9999, - "minimum": -9999 + "maximum": 180, + "minimum": 0 }, "dnarest_on": { "default": false, @@ -1071,6 +1082,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -1144,6 +1156,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -1244,6 +1257,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -1371,6 +1385,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -1525,6 +1540,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -1706,6 +1722,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -1822,6 +1839,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -1989,22 +2007,25 @@ }, "dihedflag": { "default": true, + "title": "Use torsion angle dihedral energy term", + "description": "Turns on the torsion angle dihedral energy terms of the force field.", + "$comment": "Turns on the torsion angle dihedral energy terms of the force field.", "type": "boolean" }, "sampling_factor": { "default": 1, "title": "Sampling factor for each starting model", - "description": "This paramater control how many times a model will be refined.", - "$comment": "This paramater control how many times a model will be refined. For EM refinement only it does not make sense to increase it unless random removal of restraints is turned on. If not then the energy minimisation will lead to the same final conformation.", + "description": "This parameter control how many times a model will be refined.", + "$comment": "This parameter control how many times a model will be refined. For EM refinement only it does not make sense to increase it unless random removal of restraints is turned on. If not then the energy minimisation will lead to the same final conformation.", "type": "number", - "maximum": 200, + "maximum": 500, "minimum": 1 }, "max_nmodels": { "default": 50000, "title": "Maximum number of models to refine", - "description": "This paramater controls the maximum number of models to refine.", - "$comment": "This paramater controls the maximum number of models to refine.", + "description": "This parameter controls the maximum number of models to refine.", + "$comment": "This parameter controls the maximum number of models to refine.", "type": "number", "maximum": 100000, "minimum": 1 @@ -2019,7 +2040,7 @@ "minimum": 1 }, "tolerance": { - "default": 0, + "default": 5, "title": "Failure tolerance percentage", "description": "Percentage of allowed failures for a module to successfully complete", "$comment": "Percentage of allowed failures for a module to successfully complete", @@ -2039,6 +2060,7 @@ "seg": { "type": "array", "maxItemsFrom": "molecules", + "title": "Semi-flexible segments", "items": { "type": "array", "items": { @@ -2239,217 +2261,52 @@ "maximum": 1000, "minimum": -1 }, - "nfle1": { + "nfle": { "default": 0, "title": "Number of fully flexible segments", "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", + "$comment": "This parameter defines the number of fully flexible segments for all molecules. If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables.", "type": "number", "maximum": 1000, "minimum": 0 }, "fle": { "type": "array", - "maxItemsFrom": "molecules", + "title": "Fully flexible segments", "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sta": { - "title": "Starting residue number", - "description": "Residue number defining the start of the fully flexible segment.", - "$comment": "Residue number defining the start of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - }, - "end": { - "title": "End residue number", - "description": "Residue number defining the end of the fully flexible segment.", - "$comment": "Residue number defining the end of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } + "type": "object", + "properties": { + "sta": { + "title": "Starting residue number", + "description": "Residue number defining the start of the fully flexible segment.", + "$comment": "Residue number defining the start of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" }, - "required": [], - "additionalProperties": false - } + "end": { + "title": "End residue number", + "description": "Residue number defining the end of the fully flexible segment.", + "$comment": "Residue number defining the end of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" + }, + "seg": { + "title": "Segment ID (segid)", + "description": "Segment ID of the molecule for which this flexible segment is defined.", + "$comment": "Segment ID of the molecule for which this (1st) flexible segment is defined.", + "type": "string", + "minLength": 1, + "maxLength": 4, + "format": "chain" + } + }, + "required": [], + "additionalProperties": false } - }, - "nfle2": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle3": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle4": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle5": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle6": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle7": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle8": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle9": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle10": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle11": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle12": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle13": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle14": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle15": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle16": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle17": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle18": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle19": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle20": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 } }, "required": [], @@ -2479,10 +2336,10 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_scale": { + "ambig_scale": { "ui:group": "distance restraints" }, - "unamb_scale": { + "unambig_scale": { "ui:group": "distance restraints" }, "hbond_scale": { @@ -2703,70 +2560,11 @@ "nseg20": { "ui:group": "flexibility" }, - "nfle1": { + "nfle": { "ui:group": "flexibility" }, "fle": { - "items": { - "ui:field": "table" - }, - "ui:group": "flexibility" - }, - "nfle2": { - "ui:group": "flexibility" - }, - "nfle3": { - "ui:group": "flexibility" - }, - "nfle4": { - "ui:group": "flexibility" - }, - "nfle5": { - "ui:group": "flexibility" - }, - "nfle6": { - "ui:group": "flexibility" - }, - "nfle7": { - "ui:group": "flexibility" - }, - "nfle8": { - "ui:group": "flexibility" - }, - "nfle9": { - "ui:group": "flexibility" - }, - "nfle10": { - "ui:group": "flexibility" - }, - "nfle11": { - "ui:group": "flexibility" - }, - "nfle12": { - "ui:group": "flexibility" - }, - "nfle13": { - "ui:group": "flexibility" - }, - "nfle14": { - "ui:group": "flexibility" - }, - "nfle15": { - "ui:group": "flexibility" - }, - "nfle16": { - "ui:group": "flexibility" - }, - "nfle17": { - "ui:group": "flexibility" - }, - "nfle18": { - "ui:group": "flexibility" - }, - "nfle19": { - "ui:group": "flexibility" - }, - "nfle20": { + "ui:field": "table", "ui:group": "flexibility" } }, @@ -2831,10 +2629,7 @@ "fle": { "indexed": true, "items": { - "indexed": true, - "items": { - "flatten": true - } + "flatten": true } } } @@ -2969,7 +2764,7 @@ "minimum": 1 }, "tolerance": { - "default": 0, + "default": 5, "title": "Failure tolerance percentage", "description": "Percentage of allowed failures for a module to successfully complete", "$comment": "Percentage of allowed failures for a module to successfully complete", @@ -3046,6 +2841,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -3057,6 +2853,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -3093,74 +2890,74 @@ "type": "string", "format": "uri-reference" }, - "amb_hot": { + "ambig_hot": { "default": 10, "title": "Hot phase SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "amb_cool1": { + "ambig_cool1": { "default": 10, "title": "First cooling SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "amb_cool2": { + "ambig_cool2": { "default": 50, "title": "Second cooling SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the simulatd annealing protocol. Side-chains at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the simulatd annealing protocol. Side-chains at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "amb_cool3": { + "ambig_cool3": { "default": 50, "title": "Third cooling SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the simulatd annealing protocol. Side-chains and backbone at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the simulatd annealing protocol. Side-chains and backbone at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_hot": { + "unambig_hot": { "default": 10, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_cool1": { + "unambig_cool1": { "default": 10, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_cool2": { + "unambig_cool2": { "default": 50, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_cool3": { + "unambig_cool3": { "default": 50, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3169,7 +2966,7 @@ "default": 10, "title": "Hot phase SA force constant for hbond distance restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3178,7 +2975,7 @@ "default": 10, "title": "Hot phase SA force constant for hydrogen bond restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3187,7 +2984,7 @@ "default": 50, "title": "Hot phase SA force constant for hydrogen bond restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3196,7 +2993,7 @@ "default": 50, "title": "Hot phase SA force constant for hydrogen bond restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3307,7 +3104,6 @@ "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -3322,8 +3118,8 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 9999, - "minimum": -9999 + "maximum": 180, + "minimum": 0 }, "dnarest_on": { "default": false, @@ -3366,6 +3162,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -3439,6 +3236,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -3539,6 +3337,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -3666,6 +3465,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -3820,6 +3620,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -4001,6 +3802,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -4117,6 +3919,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -4338,7 +4141,7 @@ "default": 1000, "title": "Second cooling phase SA MD steps", "description": "Number of MD steps for the second cooling phase of the SA.", - "$comment": "Number of MD steps for the second cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle_X and related parameters).", + "$comment": "Number of MD steps for the second cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters).", "type": "number", "maximum": 10000, "minimum": 0 @@ -4347,7 +4150,7 @@ "default": 1000, "title": "Third cooling phase SA MD steps", "description": "Number of MD steps for the third cooling phase of the SA.", - "$comment": "Number of MD steps for the third cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains and backbone at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle_X and related parameters).", + "$comment": "Number of MD steps for the third cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains and backbone at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters).", "type": "number", "maximum": 10000, "minimum": 0 @@ -4382,6 +4185,7 @@ "seg": { "type": "array", "maxItemsFrom": "molecules", + "title": "Semi-flexible segments", "items": { "type": "array", "items": { @@ -4582,217 +4386,52 @@ "maximum": 1000, "minimum": -1 }, - "nfle1": { + "nfle": { "default": 0, "title": "Number of fully flexible segments", "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", + "$comment": "This parameter defines the number of fully flexible segments for all molecules. If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables.", "type": "number", "maximum": 1000, "minimum": 0 }, "fle": { "type": "array", - "maxItemsFrom": "molecules", + "title": "Fully flexible segments", "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sta": { - "title": "Starting residue number", - "description": "Residue number defining the start of the fully flexible segment.", - "$comment": "Residue number defining the start of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - }, - "end": { - "title": "End residue number", - "description": "Residue number defining the end of the fully flexible segment.", - "$comment": "Residue number defining the end of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } + "type": "object", + "properties": { + "sta": { + "title": "Starting residue number", + "description": "Residue number defining the start of the fully flexible segment.", + "$comment": "Residue number defining the start of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" }, - "required": [], - "additionalProperties": false - } + "end": { + "title": "End residue number", + "description": "Residue number defining the end of the fully flexible segment.", + "$comment": "Residue number defining the end of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" + }, + "seg": { + "title": "Segment ID (segid)", + "description": "Segment ID of the molecule for which this flexible segment is defined.", + "$comment": "Segment ID of the molecule for which this (1st) flexible segment is defined.", + "type": "string", + "minLength": 1, + "maxLength": 4, + "format": "chain" + } + }, + "required": [], + "additionalProperties": false } - }, - "nfle2": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle3": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle4": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle5": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle6": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle7": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle8": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle9": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle10": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle11": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle12": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle13": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle14": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle15": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle16": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle17": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle18": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle19": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle20": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 } }, "required": [], @@ -4822,28 +4461,28 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_hot": { + "ambig_hot": { "ui:group": "distance restraints" }, - "amb_cool1": { + "ambig_cool1": { "ui:group": "distance restraints" }, - "amb_cool2": { + "ambig_cool2": { "ui:group": "distance restraints" }, - "amb_cool3": { + "ambig_cool3": { "ui:group": "distance restraints" }, - "unamb_hot": { + "unambig_hot": { "ui:group": "distance restraints" }, - "unamb_cool1": { + "unambig_cool1": { "ui:group": "distance restraints" }, - "unamb_cool2": { + "unambig_cool2": { "ui:group": "distance restraints" }, - "unamb_cool3": { + "unambig_cool3": { "ui:group": "distance restraints" }, "hbond_hot": { @@ -5106,70 +4745,11 @@ "nseg20": { "ui:group": "flexibility" }, - "nfle1": { + "nfle": { "ui:group": "flexibility" }, "fle": { - "items": { - "ui:field": "table" - }, - "ui:group": "flexibility" - }, - "nfle2": { - "ui:group": "flexibility" - }, - "nfle3": { - "ui:group": "flexibility" - }, - "nfle4": { - "ui:group": "flexibility" - }, - "nfle5": { - "ui:group": "flexibility" - }, - "nfle6": { - "ui:group": "flexibility" - }, - "nfle7": { - "ui:group": "flexibility" - }, - "nfle8": { - "ui:group": "flexibility" - }, - "nfle9": { - "ui:group": "flexibility" - }, - "nfle10": { - "ui:group": "flexibility" - }, - "nfle11": { - "ui:group": "flexibility" - }, - "nfle12": { - "ui:group": "flexibility" - }, - "nfle13": { - "ui:group": "flexibility" - }, - "nfle14": { - "ui:group": "flexibility" - }, - "nfle15": { - "ui:group": "flexibility" - }, - "nfle16": { - "ui:group": "flexibility" - }, - "nfle17": { - "ui:group": "flexibility" - }, - "nfle18": { - "ui:group": "flexibility" - }, - "nfle19": { - "ui:group": "flexibility" - }, - "nfle20": { + "ui:field": "table", "ui:group": "flexibility" } }, @@ -5234,10 +4814,7 @@ "fle": { "indexed": true, "items": { - "indexed": true, - "items": { - "flatten": true - } + "flatten": true } } } @@ -5285,10 +4862,10 @@ "format": "chain" }, "ligand_chains": { - "default": ["B"], + "default": [], "title": "Ligand ChainIDs", "description": "Ligand ChainIDs to be considered for the IL-RMSD calculations.", - "$comment": "Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be treated as the ligand for the IL-RMSD.", + "$comment": "Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be treated as the ligand for the IL-RMSD. By default, all chains are considered with the exception of the receptor chain.", "type": "array", "minItems": 0, "maxItems": 100, @@ -5490,6 +5067,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -5501,6 +5079,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -5520,7 +5099,7 @@ "default": false, "title": "Boolean condition on the previous ambiguous distance restraints file", "description": "Boolean condition on the previous ambiguous distance restraints file. If true, use the the restraint information coming from the previous CNS module. If false, don't use previous information.", - "$comment": "Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If False, don't use previous information.", + "$comment": "Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If false, don't use previous information.", "type": "boolean" }, "unambig_fname": { @@ -5537,7 +5116,7 @@ "type": "string", "format": "uri-reference" }, - "amb_scale": { + "ambig_scale": { "default": 50, "title": "Force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname.", @@ -5546,7 +5125,7 @@ "maximum": 1000, "minimum": 0 }, - "unamb_scale": { + "unambig_scale": { "default": 50, "title": "Force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname.", @@ -5639,11 +5218,10 @@ "description": "Force constant applied to the dihedral angle restraints read from dihe_fname.", "$comment": "Force constant applied to the dihedral angle restraints read from dihe_fname.", "type": "number", - "maximum": 1000, + "maximum": 9999, "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -5658,7 +5236,7 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 1000, + "maximum": 180, "minimum": 0 }, "dnarest_on": { @@ -5702,6 +5280,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -5775,6 +5354,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -5875,6 +5455,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -6002,6 +5583,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -6156,6 +5738,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -6337,6 +5920,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -6453,6 +6037,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -6631,16 +6216,16 @@ "description": "This parameter control how many times a model will be refined.", "$comment": "This parameter control how many times a model will be refined.", "type": "number", - "maximum": 400, + "maximum": 500, "minimum": 1 }, "max_nmodels": { - "default": 10000, + "default": 50000, "title": "Maximum number of models to refine", "description": "This parameter controls the maximum number of models to refine.", "$comment": "This parameter controls the maximum number of models to refine.", "type": "number", - "maximum": 50000, + "maximum": 100000, "minimum": 1 }, "solvent": { @@ -6710,6 +6295,7 @@ "seg": { "type": "array", "maxItemsFrom": "molecules", + "title": "Semi-flexible segments", "items": { "type": "array", "items": { @@ -6910,217 +6496,52 @@ "maximum": 1000, "minimum": -1 }, - "nfle1": { + "nfle": { "default": 0, "title": "Number of fully flexible segments", "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", + "$comment": "This parameter defines the number of fully flexible segments for all molecules. If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables.", "type": "number", "maximum": 1000, "minimum": 0 }, "fle": { "type": "array", - "maxItemsFrom": "molecules", + "title": "Fully flexible segments", "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sta": { - "title": "Starting residue number", - "description": "Residue number defining the start of the fully flexible segment.", - "$comment": "Residue number defining the start of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - }, - "end": { - "title": "End residue number", - "description": "Residue number defining the end of the fully flexible segment.", - "$comment": "Residue number defining the end of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } + "type": "object", + "properties": { + "sta": { + "title": "Starting residue number", + "description": "Residue number defining the start of the fully flexible segment.", + "$comment": "Residue number defining the start of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" }, - "required": [], - "additionalProperties": false - } + "end": { + "title": "End residue number", + "description": "Residue number defining the end of the fully flexible segment.", + "$comment": "Residue number defining the end of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" + }, + "seg": { + "title": "Segment ID (segid)", + "description": "Segment ID of the molecule for which this flexible segment is defined.", + "$comment": "Segment ID of the molecule for which this (1st) flexible segment is defined.", + "type": "string", + "minLength": 1, + "maxLength": 4, + "format": "chain" + } + }, + "required": [], + "additionalProperties": false } - }, - "nfle2": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle3": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle4": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle5": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle6": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle7": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle8": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle9": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle10": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle11": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle12": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle13": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle14": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle15": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle16": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle17": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle18": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle19": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle20": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 } }, "required": [], @@ -7150,10 +6571,10 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_scale": { + "ambig_scale": { "ui:group": "distance restraints" }, - "unamb_scale": { + "unambig_scale": { "ui:group": "distance restraints" }, "hbond_scale": { @@ -7392,70 +6813,11 @@ "nseg20": { "ui:group": "flexibility" }, - "nfle1": { + "nfle": { "ui:group": "flexibility" }, "fle": { - "items": { - "ui:field": "table" - }, - "ui:group": "flexibility" - }, - "nfle2": { - "ui:group": "flexibility" - }, - "nfle3": { - "ui:group": "flexibility" - }, - "nfle4": { - "ui:group": "flexibility" - }, - "nfle5": { - "ui:group": "flexibility" - }, - "nfle6": { - "ui:group": "flexibility" - }, - "nfle7": { - "ui:group": "flexibility" - }, - "nfle8": { - "ui:group": "flexibility" - }, - "nfle9": { - "ui:group": "flexibility" - }, - "nfle10": { - "ui:group": "flexibility" - }, - "nfle11": { - "ui:group": "flexibility" - }, - "nfle12": { - "ui:group": "flexibility" - }, - "nfle13": { - "ui:group": "flexibility" - }, - "nfle14": { - "ui:group": "flexibility" - }, - "nfle15": { - "ui:group": "flexibility" - }, - "nfle16": { - "ui:group": "flexibility" - }, - "nfle17": { - "ui:group": "flexibility" - }, - "nfle18": { - "ui:group": "flexibility" - }, - "nfle19": { - "ui:group": "flexibility" - }, - "nfle20": { + "ui:field": "table", "ui:group": "flexibility" } }, @@ -7520,10 +6882,7 @@ "fle": { "indexed": true, "items": { - "indexed": true, - "items": { - "flatten": true - } + "flatten": true } } } @@ -7574,7 +6933,7 @@ "default": 0.2, "title": "Weight of the intermolecular electrostatic energy", "description": "Weight of the intermolecular electrostatic energy in the scoring function", - "$comment": "Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the EM minimization.", + "$comment": "Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the MD refinement.", "type": "number", "maximum": 9999, "minimum": -9999 @@ -7605,7 +6964,6 @@ "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -7672,6 +7030,9 @@ }, "dihedflag": { "default": true, + "title": "Use torsion angle dihedral energy term", + "description": "Turns on the torsion angle dihedral energy terms of the force field.", + "$comment": "Turns on the torsion angle dihedral energy terms of the force field.", "type": "boolean" }, "individualize": { @@ -7826,6 +7187,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -7837,6 +7199,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -7873,7 +7236,7 @@ "type": "string", "format": "uri-reference" }, - "amb_scale": { + "ambig_scale": { "default": 50, "title": "Force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname.", @@ -7882,7 +7245,7 @@ "maximum": 1000, "minimum": 0 }, - "unamb_scale": { + "unambig_scale": { "default": 50, "title": "Force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname.", @@ -8052,7 +7415,7 @@ "minimum": 0 }, "tolerance": { - "default": 0, + "default": 5, "title": "Failure tolerance percentage", "description": "Percentage of allowed failures for a module to successfully complete", "$comment": "Percentage of allowed failures for a module to successfully complete", @@ -8094,6 +7457,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -8167,6 +7531,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -8267,6 +7632,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -8394,6 +7760,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -8548,6 +7915,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -8729,6 +8097,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -8845,6 +8214,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -9047,10 +8417,10 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_scale": { + "ambig_scale": { "ui:group": "distance restraints" }, - "unamb_scale": { + "unambig_scale": { "ui:group": "distance restraints" }, "hbond_scale": { @@ -9524,6 +8894,7 @@ }, "hisd": { "type": "array", + "title": "Histidines to be defined as HISD", "items": { "title": "HISD residue number", "description": "Residue number of the Histidine to be defined as HISD", @@ -9545,6 +8916,7 @@ }, "hise": { "type": "array", + "title": "Histidines to be defined as HISE", "items": { "title": "HISE residue number", "description": "Residue number of the Histidine to be defined as HISE", diff --git a/app/catalogs/haddock3.guru.json b/app/catalogs/haddock3.guru.json index e68a0468..48da09a3 100644 --- a/app/catalogs/haddock3.guru.json +++ b/app/catalogs/haddock3.guru.json @@ -413,6 +413,13 @@ "$comment": "Evaluate DockQ. A single continuous quality measure for protein docked models based on the CAPRI criteria, a combination of i-RMSD, l-RMSD and FNAT value. For details check the DockQ publication `DOI:10.1371/journal.pone.0161879`", "type": "boolean" }, + "global_rmsd": { + "default": true, + "title": "Calculate global RMSD", + "description": "Calculate full structure RMSD.", + "$comment": "Compute full structure RMSD between reference structure and the model after superimposition. Note that a sequence alignment is performed to obtain the mapping between the reference and the model. If the one of the structure contain a 'small-molecule', we assume that the compared structure atoms are in the same order. With default parameters `allatoms = false`, only backbone RMSD will be computed.", + "type": "boolean" + }, "irmsd_cutoff": { "default": 10, "title": "Distance cutoff (Å) used to define interface residues.", @@ -442,7 +449,7 @@ "format": "chain" }, "ligand_chains": { - "default": ["B"], + "default": [], "title": "Ligand ChainIDs", "description": "Ligand ChainIDs to be considered for the RMSD calculations.", "$comment": "Ligand ChainIDs to be considered for the RMSD calculations. This determines which chains will be treated as the ligand for the L-RMSD and for I-L-RMSD.", @@ -529,6 +536,9 @@ "dockq": { "ui:group": "analysis" }, + "global_rmsd": { + "ui:group": "analysis" + }, "irmsd_cutoff": { "ui:group": "analysis" }, @@ -892,6 +902,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -903,6 +914,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -939,7 +951,7 @@ "type": "string", "format": "uri-reference" }, - "amb_scale": { + "ambig_scale": { "default": 50, "title": "Force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname.", @@ -948,7 +960,7 @@ "maximum": 1000, "minimum": 0 }, - "unamb_scale": { + "unambig_scale": { "default": 50, "title": "Force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname.", @@ -1019,10 +1031,9 @@ "$comment": "Force constant applied to the dihedral angle restraints read from dihe_fname.", "type": "number", "maximum": 9999, - "minimum": -9999 + "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -1037,8 +1048,8 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 9999, - "minimum": -9999 + "maximum": 180, + "minimum": 0 }, "dnarest_on": { "default": false, @@ -1081,6 +1092,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -1154,6 +1166,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -1254,6 +1267,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -1381,6 +1395,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -1535,6 +1550,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -1716,6 +1732,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -1832,6 +1849,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -1999,22 +2017,25 @@ }, "dihedflag": { "default": true, + "title": "Use torsion angle dihedral energy term", + "description": "Turns on the torsion angle dihedral energy terms of the force field.", + "$comment": "Turns on the torsion angle dihedral energy terms of the force field.", "type": "boolean" }, "sampling_factor": { "default": 1, "title": "Sampling factor for each starting model", - "description": "This paramater control how many times a model will be refined.", - "$comment": "This paramater control how many times a model will be refined. For EM refinement only it does not make sense to increase it unless random removal of restraints is turned on. If not then the energy minimisation will lead to the same final conformation.", + "description": "This parameter control how many times a model will be refined.", + "$comment": "This parameter control how many times a model will be refined. For EM refinement only it does not make sense to increase it unless random removal of restraints is turned on. If not then the energy minimisation will lead to the same final conformation.", "type": "number", - "maximum": 200, + "maximum": 500, "minimum": 1 }, "max_nmodels": { "default": 50000, "title": "Maximum number of models to refine", - "description": "This paramater controls the maximum number of models to refine.", - "$comment": "This paramater controls the maximum number of models to refine.", + "description": "This parameter controls the maximum number of models to refine.", + "$comment": "This parameter controls the maximum number of models to refine.", "type": "number", "maximum": 100000, "minimum": 1 @@ -2045,7 +2066,7 @@ "type": "boolean" }, "tolerance": { - "default": 0, + "default": 5, "title": "Failure tolerance percentage", "description": "Percentage of allowed failures for a module to successfully complete", "$comment": "Percentage of allowed failures for a module to successfully complete", @@ -2057,7 +2078,7 @@ "default": "quiet", "title": "Log level verbosity for CNS", "description": "Set the log level verbosity for CNS", - "$comment": "CNS, the computational engine used by HADDOCK can generate a lot of output messages. This parameter controls the verbosity of CNS (verbose, normal or quiet)", + "$comment": "CNS, the computational engine used by HADDOCK can generate a lot of output messages. This parameter controls the verbosity of CNS (verbose, normal or quiet).", "type": "string", "minLength": 0, "maxLength": 100, @@ -2075,6 +2096,7 @@ "seg": { "type": "array", "maxItemsFrom": "molecules", + "title": "Semi-flexible segments", "items": { "type": "array", "items": { @@ -2275,217 +2297,52 @@ "maximum": 1000, "minimum": -1 }, - "nfle1": { + "nfle": { "default": 0, "title": "Number of fully flexible segments", "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", + "$comment": "This parameter defines the number of fully flexible segments for all molecules. If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables.", "type": "number", "maximum": 1000, "minimum": 0 }, "fle": { "type": "array", - "maxItemsFrom": "molecules", + "title": "Fully flexible segments", "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sta": { - "title": "Starting residue number", - "description": "Residue number defining the start of the fully flexible segment.", - "$comment": "Residue number defining the start of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - }, - "end": { - "title": "End residue number", - "description": "Residue number defining the end of the fully flexible segment.", - "$comment": "Residue number defining the end of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } + "type": "object", + "properties": { + "sta": { + "title": "Starting residue number", + "description": "Residue number defining the start of the fully flexible segment.", + "$comment": "Residue number defining the start of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" }, - "required": [], - "additionalProperties": false - } + "end": { + "title": "End residue number", + "description": "Residue number defining the end of the fully flexible segment.", + "$comment": "Residue number defining the end of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" + }, + "seg": { + "title": "Segment ID (segid)", + "description": "Segment ID of the molecule for which this flexible segment is defined.", + "$comment": "Segment ID of the molecule for which this (1st) flexible segment is defined.", + "type": "string", + "minLength": 1, + "maxLength": 4, + "format": "chain" + } + }, + "required": [], + "additionalProperties": false } - }, - "nfle2": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle3": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle4": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle5": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle6": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle7": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle8": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle9": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle10": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle11": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle12": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle13": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle14": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle15": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle16": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle17": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle18": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle19": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle20": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 } }, "required": [], @@ -2515,10 +2372,10 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_scale": { + "ambig_scale": { "ui:group": "distance restraints" }, - "unamb_scale": { + "unambig_scale": { "ui:group": "distance restraints" }, "hbond_scale": { @@ -2748,70 +2605,11 @@ "nseg20": { "ui:group": "flexibility" }, - "nfle1": { + "nfle": { "ui:group": "flexibility" }, "fle": { - "items": { - "ui:field": "table" - }, - "ui:group": "flexibility" - }, - "nfle2": { - "ui:group": "flexibility" - }, - "nfle3": { - "ui:group": "flexibility" - }, - "nfle4": { - "ui:group": "flexibility" - }, - "nfle5": { - "ui:group": "flexibility" - }, - "nfle6": { - "ui:group": "flexibility" - }, - "nfle7": { - "ui:group": "flexibility" - }, - "nfle8": { - "ui:group": "flexibility" - }, - "nfle9": { - "ui:group": "flexibility" - }, - "nfle10": { - "ui:group": "flexibility" - }, - "nfle11": { - "ui:group": "flexibility" - }, - "nfle12": { - "ui:group": "flexibility" - }, - "nfle13": { - "ui:group": "flexibility" - }, - "nfle14": { - "ui:group": "flexibility" - }, - "nfle15": { - "ui:group": "flexibility" - }, - "nfle16": { - "ui:group": "flexibility" - }, - "nfle17": { - "ui:group": "flexibility" - }, - "nfle18": { - "ui:group": "flexibility" - }, - "nfle19": { - "ui:group": "flexibility" - }, - "nfle20": { + "ui:field": "table", "ui:group": "flexibility" } }, @@ -2876,10 +2674,7 @@ "fle": { "indexed": true, "items": { - "indexed": true, - "items": { - "flatten": true - } + "flatten": true } } } @@ -3014,7 +2809,7 @@ "minimum": 1 }, "tolerance": { - "default": 0, + "default": 5, "title": "Failure tolerance percentage", "description": "Percentage of allowed failures for a module to successfully complete", "$comment": "Percentage of allowed failures for a module to successfully complete", @@ -3104,6 +2899,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -3115,6 +2911,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -3151,74 +2948,74 @@ "type": "string", "format": "uri-reference" }, - "amb_hot": { + "ambig_hot": { "default": 10, "title": "Hot phase SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "amb_cool1": { + "ambig_cool1": { "default": 10, "title": "First cooling SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "amb_cool2": { + "ambig_cool2": { "default": 50, "title": "Second cooling SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the simulatd annealing protocol. Side-chains at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the simulatd annealing protocol. Side-chains at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "amb_cool3": { + "ambig_cool3": { "default": 50, "title": "Third cooling SA force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the simulatd annealing protocol. Side-chains and backbone at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the simulatd annealing protocol. Side-chains and backbone at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_hot": { + "unambig_hot": { "default": 10, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_cool1": { + "unambig_cool1": { "default": 10, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_cool2": { + "unambig_cool2": { "default": 50, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 }, - "unamb_cool3": { + "unambig_cool3": { "default": 50, "title": "Hot phase SA force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3227,7 +3024,7 @@ "default": 10, "title": "Hot phase SA force constant for hbond distance restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3236,7 +3033,7 @@ "default": 10, "title": "Hot phase SA force constant for hydrogen bond restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3245,7 +3042,7 @@ "default": 50, "title": "Hot phase SA force constant for hydrogen bond restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3254,7 +3051,7 @@ "default": 50, "title": "Hot phase SA force constant for hydrogen bond restraints", "description": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.", - "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle_X parameter).", + "$comment": "Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).", "type": "number", "maximum": 1000, "minimum": 0 @@ -3365,7 +3162,6 @@ "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -3380,8 +3176,8 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 9999, - "minimum": -9999 + "maximum": 180, + "minimum": 0 }, "dnarest_on": { "default": false, @@ -3424,6 +3220,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -3497,6 +3294,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -3597,6 +3395,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -3724,6 +3523,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -3878,6 +3678,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -4059,6 +3860,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -4175,6 +3977,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -4396,7 +4199,7 @@ "default": 1000, "title": "Second cooling phase SA MD steps", "description": "Number of MD steps for the second cooling phase of the SA.", - "$comment": "Number of MD steps for the second cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle_X and related parameters).", + "$comment": "Number of MD steps for the second cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters).", "type": "number", "maximum": 10000, "minimum": 0 @@ -4405,7 +4208,7 @@ "default": 1000, "title": "Third cooling phase SA MD steps", "description": "Number of MD steps for the third cooling phase of the SA.", - "$comment": "Number of MD steps for the third cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains and backbone at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle_X and related parameters).", + "$comment": "Number of MD steps for the third cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains and backbone at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters).", "type": "number", "maximum": 10000, "minimum": 0 @@ -4599,6 +4402,7 @@ "seg": { "type": "array", "maxItemsFrom": "molecules", + "title": "Semi-flexible segments", "items": { "type": "array", "items": { @@ -4799,217 +4603,52 @@ "maximum": 1000, "minimum": -1 }, - "nfle1": { + "nfle": { "default": 0, "title": "Number of fully flexible segments", "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", + "$comment": "This parameter defines the number of fully flexible segments for all molecules. If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables.", "type": "number", "maximum": 1000, "minimum": 0 }, "fle": { "type": "array", - "maxItemsFrom": "molecules", + "title": "Fully flexible segments", "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sta": { - "title": "Starting residue number", - "description": "Residue number defining the start of the fully flexible segment.", - "$comment": "Residue number defining the start of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - }, - "end": { - "title": "End residue number", - "description": "Residue number defining the end of the fully flexible segment.", - "$comment": "Residue number defining the end of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } + "type": "object", + "properties": { + "sta": { + "title": "Starting residue number", + "description": "Residue number defining the start of the fully flexible segment.", + "$comment": "Residue number defining the start of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" }, - "required": [], - "additionalProperties": false - } + "end": { + "title": "End residue number", + "description": "Residue number defining the end of the fully flexible segment.", + "$comment": "Residue number defining the end of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" + }, + "seg": { + "title": "Segment ID (segid)", + "description": "Segment ID of the molecule for which this flexible segment is defined.", + "$comment": "Segment ID of the molecule for which this (1st) flexible segment is defined.", + "type": "string", + "minLength": 1, + "maxLength": 4, + "format": "chain" + } + }, + "required": [], + "additionalProperties": false } - }, - "nfle2": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle3": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle4": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle5": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle6": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle7": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle8": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle9": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle10": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle11": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle12": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle13": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle14": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle15": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle16": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle17": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle18": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle19": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle20": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 } }, "required": [], @@ -5039,28 +4678,28 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_hot": { + "ambig_hot": { "ui:group": "distance restraints" }, - "amb_cool1": { + "ambig_cool1": { "ui:group": "distance restraints" }, - "amb_cool2": { + "ambig_cool2": { "ui:group": "distance restraints" }, - "amb_cool3": { + "ambig_cool3": { "ui:group": "distance restraints" }, - "unamb_hot": { + "unambig_hot": { "ui:group": "distance restraints" }, - "unamb_cool1": { + "unambig_cool1": { "ui:group": "distance restraints" }, - "unamb_cool2": { + "unambig_cool2": { "ui:group": "distance restraints" }, - "unamb_cool3": { + "unambig_cool3": { "ui:group": "distance restraints" }, "hbond_hot": { @@ -5374,73 +5013,14 @@ "nseg19": { "ui:group": "flexibility" }, - "nseg20": { - "ui:group": "flexibility" - }, - "nfle1": { - "ui:group": "flexibility" - }, - "fle": { - "items": { - "ui:field": "table" - }, - "ui:group": "flexibility" - }, - "nfle2": { - "ui:group": "flexibility" - }, - "nfle3": { - "ui:group": "flexibility" - }, - "nfle4": { - "ui:group": "flexibility" - }, - "nfle5": { - "ui:group": "flexibility" - }, - "nfle6": { - "ui:group": "flexibility" - }, - "nfle7": { - "ui:group": "flexibility" - }, - "nfle8": { - "ui:group": "flexibility" - }, - "nfle9": { - "ui:group": "flexibility" - }, - "nfle10": { - "ui:group": "flexibility" - }, - "nfle11": { - "ui:group": "flexibility" - }, - "nfle12": { - "ui:group": "flexibility" - }, - "nfle13": { - "ui:group": "flexibility" - }, - "nfle14": { - "ui:group": "flexibility" - }, - "nfle15": { - "ui:group": "flexibility" - }, - "nfle16": { - "ui:group": "flexibility" - }, - "nfle17": { - "ui:group": "flexibility" - }, - "nfle18": { + "nseg20": { "ui:group": "flexibility" }, - "nfle19": { + "nfle": { "ui:group": "flexibility" }, - "nfle20": { + "fle": { + "ui:field": "table", "ui:group": "flexibility" } }, @@ -5505,10 +5085,7 @@ "fle": { "indexed": true, "items": { - "indexed": true, - "items": { - "flatten": true - } + "flatten": true } } } @@ -5556,10 +5133,10 @@ "format": "chain" }, "ligand_chains": { - "default": ["B"], + "default": [], "title": "Ligand ChainIDs", "description": "Ligand ChainIDs to be considered for the IL-RMSD calculations.", - "$comment": "Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be treated as the ligand for the IL-RMSD.", + "$comment": "Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be treated as the ligand for the IL-RMSD. By default, all chains are considered with the exception of the receptor chain.", "type": "array", "minItems": 0, "maxItems": 100, @@ -5773,6 +5350,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -5784,6 +5362,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -5803,7 +5382,7 @@ "default": false, "title": "Boolean condition on the previous ambiguous distance restraints file", "description": "Boolean condition on the previous ambiguous distance restraints file. If true, use the the restraint information coming from the previous CNS module. If false, don't use previous information.", - "$comment": "Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If False, don't use previous information.", + "$comment": "Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If false, don't use previous information.", "type": "boolean" }, "unambig_fname": { @@ -5820,7 +5399,7 @@ "type": "string", "format": "uri-reference" }, - "amb_scale": { + "ambig_scale": { "default": 50, "title": "Force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname.", @@ -5829,7 +5408,7 @@ "maximum": 1000, "minimum": 0 }, - "unamb_scale": { + "unambig_scale": { "default": 50, "title": "Force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname.", @@ -5922,11 +5501,10 @@ "description": "Force constant applied to the dihedral angle restraints read from dihe_fname.", "$comment": "Force constant applied to the dihedral angle restraints read from dihe_fname.", "type": "number", - "maximum": 1000, + "maximum": 9999, "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -5941,7 +5519,7 @@ "description": "Force constant for backbone dihedral angle restraints (ssdihed option)", "$comment": "Force constant for backbone dihedral angle restraints (ssdihed option)", "type": "number", - "maximum": 1000, + "maximum": 180, "minimum": 0 }, "dnarest_on": { @@ -5985,6 +5563,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -6058,6 +5637,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -6158,6 +5738,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -6285,6 +5866,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -6439,6 +6021,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -6620,6 +6203,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -6736,6 +6320,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -6914,16 +6499,16 @@ "description": "This parameter control how many times a model will be refined.", "$comment": "This parameter control how many times a model will be refined.", "type": "number", - "maximum": 400, + "maximum": 500, "minimum": 1 }, "max_nmodels": { - "default": 10000, + "default": 50000, "title": "Maximum number of models to refine", "description": "This parameter controls the maximum number of models to refine.", "$comment": "This parameter controls the maximum number of models to refine.", "type": "number", - "maximum": 50000, + "maximum": 100000, "minimum": 1 }, "solvent": { @@ -7028,6 +6613,7 @@ "seg": { "type": "array", "maxItemsFrom": "molecules", + "title": "Semi-flexible segments", "items": { "type": "array", "items": { @@ -7228,217 +6814,52 @@ "maximum": 1000, "minimum": -1 }, - "nfle1": { + "nfle": { "default": 0, "title": "Number of fully flexible segments", "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", + "$comment": "This parameter defines the number of fully flexible segments for all molecules. If >=1 then those must be defined manually with segment ID (segid) in the fle_seg_* variable, followed by the starting and ending residue numbers in the fle_sta_* and fle_end_* variables.", "type": "number", "maximum": 1000, "minimum": 0 }, "fle": { "type": "array", - "maxItemsFrom": "molecules", + "title": "Fully flexible segments", "items": { - "type": "array", - "items": { - "type": "object", - "properties": { - "sta": { - "title": "Starting residue number", - "description": "Residue number defining the start of the fully flexible segment.", - "$comment": "Residue number defining the start of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - }, - "end": { - "title": "End residue number", - "description": "Residue number defining the end of the fully flexible segment.", - "$comment": "Residue number defining the end of the fully flexible segment.", - "type": "number", - "maximum": 9999, - "minimum": -9999, - "format": "residue" - } + "type": "object", + "properties": { + "sta": { + "title": "Starting residue number", + "description": "Residue number defining the start of the fully flexible segment.", + "$comment": "Residue number defining the start of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" }, - "required": [], - "additionalProperties": false - } + "end": { + "title": "End residue number", + "description": "Residue number defining the end of the fully flexible segment.", + "$comment": "Residue number defining the end of this (1st) fully flexible segment.", + "type": "number", + "maximum": 9999, + "minimum": -9999, + "format": "residue" + }, + "seg": { + "title": "Segment ID (segid)", + "description": "Segment ID of the molecule for which this flexible segment is defined.", + "$comment": "Segment ID of the molecule for which this (1st) flexible segment is defined.", + "type": "string", + "minLength": 1, + "maxLength": 4, + "format": "chain" + } + }, + "required": [], + "additionalProperties": false } - }, - "nfle2": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle3": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle4": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle5": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle6": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle7": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle8": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle9": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle10": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle11": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle12": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle13": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle14": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle15": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle16": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle17": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle18": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle19": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 - }, - "nfle20": { - "default": 0, - "title": "Number of fully flexible segments", - "description": "This defines the number of fully flexible segments.", - "$comment": "This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.", - "type": "number", - "maximum": 1000, - "minimum": 0 } }, "required": [], @@ -7468,10 +6889,10 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_scale": { + "ambig_scale": { "ui:group": "distance restraints" }, - "unamb_scale": { + "unambig_scale": { "ui:group": "distance restraints" }, "hbond_scale": { @@ -7722,70 +7143,11 @@ "nseg20": { "ui:group": "flexibility" }, - "nfle1": { + "nfle": { "ui:group": "flexibility" }, "fle": { - "items": { - "ui:field": "table" - }, - "ui:group": "flexibility" - }, - "nfle2": { - "ui:group": "flexibility" - }, - "nfle3": { - "ui:group": "flexibility" - }, - "nfle4": { - "ui:group": "flexibility" - }, - "nfle5": { - "ui:group": "flexibility" - }, - "nfle6": { - "ui:group": "flexibility" - }, - "nfle7": { - "ui:group": "flexibility" - }, - "nfle8": { - "ui:group": "flexibility" - }, - "nfle9": { - "ui:group": "flexibility" - }, - "nfle10": { - "ui:group": "flexibility" - }, - "nfle11": { - "ui:group": "flexibility" - }, - "nfle12": { - "ui:group": "flexibility" - }, - "nfle13": { - "ui:group": "flexibility" - }, - "nfle14": { - "ui:group": "flexibility" - }, - "nfle15": { - "ui:group": "flexibility" - }, - "nfle16": { - "ui:group": "flexibility" - }, - "nfle17": { - "ui:group": "flexibility" - }, - "nfle18": { - "ui:group": "flexibility" - }, - "nfle19": { - "ui:group": "flexibility" - }, - "nfle20": { + "ui:field": "table", "ui:group": "flexibility" } }, @@ -7850,10 +7212,7 @@ "fle": { "indexed": true, "items": { - "indexed": true, - "items": { - "flatten": true - } + "flatten": true } } } @@ -7904,7 +7263,7 @@ "default": 0.2, "title": "Weight of the intermolecular electrostatic energy", "description": "Weight of the intermolecular electrostatic energy in the scoring function", - "$comment": "Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the EM minimization.", + "$comment": "Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the MD refinement.", "type": "number", "maximum": 9999, "minimum": -9999 @@ -7935,7 +7294,6 @@ "minimum": 0 }, "ssdihed": { - "default": "none", "title": "Define automatically backbone dihedral angle restraints", "description": "If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.", "$comment": "This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.", @@ -8002,6 +7360,9 @@ }, "dihedflag": { "default": true, + "title": "Use torsion angle dihedral energy term", + "description": "Turns on the torsion angle dihedral energy terms of the force field.", + "$comment": "Turns on the torsion angle dihedral energy terms of the force field.", "type": "boolean" }, "individualize": { @@ -8203,6 +7564,7 @@ "mol_fix_origin": { "type": "array", "maxItemsFrom": "molecules", + "title": "Fix origin(s)", "items": { "default": false, "title": "Fix molecule", @@ -8214,6 +7576,7 @@ "mol_shape": { "type": "array", "maxItemsFrom": "molecules", + "title": "Shape(s)", "items": { "default": false, "title": "Is the molecule a shape?", @@ -8250,7 +7613,7 @@ "type": "string", "format": "uri-reference" }, - "amb_scale": { + "ambig_scale": { "default": 50, "title": "Force constant for ambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in ambig_fname.", @@ -8259,7 +7622,7 @@ "maximum": 1000, "minimum": 0 }, - "unamb_scale": { + "unambig_scale": { "default": 50, "title": "Force constant for unambiguous distance restraints", "description": "Force constant applied to the distance restraints defined in unambig_fname.", @@ -8452,7 +7815,7 @@ "minimum": 0 }, "tolerance": { - "default": 0, + "default": 5, "title": "Failure tolerance percentage", "description": "Percentage of allowed failures for a module to successfully complete", "$comment": "Percentage of allowed failures for a module to successfully complete", @@ -8504,6 +7867,7 @@ }, "c2sym": { "type": "array", + "title": "C2 symmetry restraints", "items": { "type": "object", "properties": { @@ -8577,6 +7941,7 @@ }, "c3sym": { "type": "array", + "title": "C3 symmetry restraints", "items": { "type": "object", "properties": { @@ -8677,6 +8042,7 @@ }, "c4sym": { "type": "array", + "title": "C4 symmetry restraints", "items": { "type": "object", "properties": { @@ -8804,6 +8170,7 @@ }, "c5sym": { "type": "array", + "title": "C5 symmetry restraints", "items": { "type": "object", "properties": { @@ -8958,6 +8325,7 @@ }, "c6sym": { "type": "array", + "title": "C6 symmetry restraints", "items": { "type": "object", "properties": { @@ -9139,6 +8507,7 @@ }, "s3sym": { "type": "array", + "title": "S3 symmetry restraints", "items": { "type": "object", "properties": { @@ -9255,6 +8624,7 @@ }, "ncs": { "type": "array", + "title": "Non-crystallographic symmetry restraints", "items": { "type": "object", "properties": { @@ -9457,10 +8827,10 @@ "ui:widget": "file", "ui:group": "distance restraints" }, - "amb_scale": { + "ambig_scale": { "ui:group": "distance restraints" }, - "unamb_scale": { + "unambig_scale": { "ui:group": "distance restraints" }, "hbond_scale": { @@ -9940,6 +9310,24 @@ "maximum": 99, "minimum": 0 }, + "cyclicpept_dist": { + "default": 2, + "title": "Cutoff distance for cyclisation", + "description": "Cutoff distance in Angstroms for identification of backbone cyclic peptide", + "$comment": "Cutoff distance in Angstroms for identification of backbone cyclic peptide (N - C)", + "type": "number", + "maximum": 999999.99, + "minimum": 0 + }, + "disulphide_dist": { + "default": 2.2, + "title": "Cutoff distance for S-S bonds", + "description": "Cutoff distance in Angstroms for identification of disulphide bonds", + "$comment": "Cutoff distance in Angstroms for identification of disulphide bonds (SH - SH)", + "type": "number", + "maximum": 999999.99, + "minimum": 0 + }, "mol": { "title": "Input molecule configuration", "$comment": "You can expand this parameter and associated sub-parameters to the other input molecules. For example, if you input three molecules, you can define mol1, mol2, and mol3 subparameters. Those not defined will be populated with the defaults.", @@ -9965,6 +9353,7 @@ }, "hisd": { "type": "array", + "title": "Histidines to be defined as HISD", "items": { "title": "HISD residue number", "description": "Residue number of the Histidine to be defined as HISD", @@ -9986,6 +9375,7 @@ }, "hise": { "type": "array", + "title": "Histidines to be defined as HISE", "items": { "title": "HISE residue number", "description": "Residue number of the Histidine to be defined as HISE", @@ -10036,6 +9426,12 @@ "tolerance": { "ui:group": "module" }, + "cyclicpept_dist": { + "ui:group": "molecule" + }, + "disulphide_dist": { + "ui:group": "molecule" + }, "mol": { "ui:indexable": true, "ui:group": "input molecules" From 6130de2248864585c65281debc22ce389b1aa880 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Mon, 16 Sep 2024 14:41:03 +0200 Subject: [PATCH 2/4] Allow easy expertise level to run protein ligand scenario As https://github.com/haddocking/haddock3/issues/914 has been fixed. --- app/routes/scenarios.protein-ligand.tsx | 13 +--- .../HeteroMoleculeSubForm.client.tsx | 68 +++++-------------- 2 files changed, 20 insertions(+), 61 deletions(-) diff --git a/app/routes/scenarios.protein-ligand.tsx b/app/routes/scenarios.protein-ligand.tsx index d8f6b07c..349156fd 100644 --- a/app/routes/scenarios.protein-ligand.tsx +++ b/app/routes/scenarios.protein-ligand.tsx @@ -4,7 +4,6 @@ import { useSubmit, useNavigate, json, - useLoaderData, } from "@remix-run/react"; import { object, @@ -42,14 +41,8 @@ import { BindingMoleculeSubForm } from "~/scenarios/BindingMoleculeSubForm.clien import { ReferenceStructureInput } from "~/scenarios/ReferenceStructureInput"; export const loader = async ({ request }: LoaderFunctionArgs) => { - const user = await mustBeAllowedToSubmit(request); - // Only expert and higher can use custom ligand files - // See https://www.bonvinlab.org/haddock3/modules/topology/haddock.modules.topology.topoaa.html#ligand-param-fname - return json({ - mayUseCustomLigandFiles: - user.preferredExpertiseLevel !== null && - ["expert", "guru"].includes(user.preferredExpertiseLevel), - }); + await mustBeAllowedToSubmit(request); + return json({}); }; export const action = uploadaction; @@ -201,7 +194,6 @@ async function createZip(workflow: string, data: Schema) { } export default function Page() { - const { mayUseCustomLigandFiles } = useLoaderData(); const actionData = useActionData(); const submit = useSubmit(); const navigate = useNavigate(); @@ -322,7 +314,6 @@ export default function Page() { actpass={ligandActPass} onActPassChange={setLigandActPass} targetChain="B" - mayUseCustomLigandFiles={mayUseCustomLigandFiles} /> diff --git a/app/scenarios/HeteroMoleculeSubForm.client.tsx b/app/scenarios/HeteroMoleculeSubForm.client.tsx index c19a742e..1c4db1da 100644 --- a/app/scenarios/HeteroMoleculeSubForm.client.tsx +++ b/app/scenarios/HeteroMoleculeSubForm.client.tsx @@ -186,7 +186,6 @@ export function HeteroMoleculeSubForm({ actpass, onActPassChange, targetChain, - mayUseCustomLigandFiles, }: { name: string; legend: string; @@ -194,37 +193,10 @@ export function HeteroMoleculeSubForm({ actpass: ActPassSelection; onActPassChange: (actpass: ActPassSelection) => void; targetChain: string; - mayUseCustomLigandFiles: boolean; }) { const [processedFile, setProcessedFile] = useState(); const [selected, setSelected] = useState(); - // TODO remove if once https://github.com/haddocking/haddock3/issues/914 is fixed - if (!mayUseCustomLigandFiles) { - return ( - -
-

- Your expertise level is to low to set all the parameters needed for - a ligand. -

-

- Once{" "} - - haddock3 issue #914 - {" "} - is solved, you will be allowed use this scenario. -

-
- - ); - } - async function onSelect(newSelected: Hetero, file: File) { const pdbWithSingleHet = await hetGrepFile( file, @@ -293,28 +265,24 @@ export function HeteroMoleculeSubForm({ )} - {mayUseCustomLigandFiles && ( - <> - - - - - - - - )} + + + + + + ); } From f7643679be1b6c10a1385543a65f2df0e1bf3a89 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Mon, 16 Sep 2024 12:54:23 +0000 Subject: [PATCH 3/4] Format --- app/routes/scenarios.protein-ligand.tsx | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/app/routes/scenarios.protein-ligand.tsx b/app/routes/scenarios.protein-ligand.tsx index 349156fd..3df28f27 100644 --- a/app/routes/scenarios.protein-ligand.tsx +++ b/app/routes/scenarios.protein-ligand.tsx @@ -1,10 +1,5 @@ import { useState } from "react"; -import { - useActionData, - useSubmit, - useNavigate, - json, -} from "@remix-run/react"; +import { useActionData, useSubmit, useNavigate, json } from "@remix-run/react"; import { object, instance, From 3a759a7a3810570fa0062aa2201ec582d057733f Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Mon, 16 Sep 2024 19:00:22 +0200 Subject: [PATCH 4/4] Sync catalog and haddock3 versions --- deploy/Dockerfile.bartenderhaddock3 | 2 +- deploy/containerslurm/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/deploy/Dockerfile.bartenderhaddock3 b/deploy/Dockerfile.bartenderhaddock3 index 9fff8cf9..0c0d7b01 100644 --- a/deploy/Dockerfile.bartenderhaddock3 +++ b/deploy/Dockerfile.bartenderhaddock3 @@ -48,7 +48,7 @@ RUN pip install . # haddock3 ============================================================================================================ WORKDIR /opt/haddock3 -RUN echo cachebust=3 && git clone --depth 1 -b ${HADDOCK3_VERSION} --recursive https://github.com/${HADDOCK3_GHORG}/haddock3.git . +RUN echo cachebust=6 && git clone --depth 1 -b ${HADDOCK3_VERSION} --recursive https://github.com/${HADDOCK3_GHORG}/haddock3.git . WORKDIR /opt/haddock3/src/fcc/src RUN make WORKDIR /opt/haddock3/src/fast-rmsdmatrix/src diff --git a/deploy/containerslurm/Dockerfile b/deploy/containerslurm/Dockerfile index fd7262e6..49b48f56 100644 --- a/deploy/containerslurm/Dockerfile +++ b/deploy/containerslurm/Dockerfile @@ -42,7 +42,7 @@ ENV GDOCK_PATH=/opt/gdock # haddock3 ============================================================================================================ WORKDIR /opt/haddock3 -RUN echo cachebust=2 && git clone --depth 1 -b ${HADDOCK3_VERSION} --recursive https://github.com/${HADDOCK3_GHORG}/haddock3.git . +RUN echo cachebust=6 && git clone --depth 1 -b ${HADDOCK3_VERSION} --recursive https://github.com/${HADDOCK3_GHORG}/haddock3.git . WORKDIR /opt/haddock3/src/fcc/src RUN make WORKDIR /opt/haddock3/src/fast-rmsdmatrix/src