Real Space 3 Download [PORTABLE] Full Versionl
Abstract:We develop a real space cluster extension of the typical medium theory (cluster-TMT) to study Anderson localization. By construction, the cluster-TMT approach is formally equivalent to the real space cluster extension of the dynamical mean field theory. Applying the developed method to the 3D Anderson model with a box disorder distribution, we demonstrate that cluster-TMT successfully captures the localization phenomena in all disorder regimes. As a function of the cluster size, our method obtains the correct critical disorder strength for the Anderson localization in 3D, and systematically recovers the re-entrance behavior of the mobility edge. From a general perspective, our developed methodology offers the potential to study Anderson localization at surfaces within quantum embedding theory. This opens the door to studying the interplay between topology and Anderson localization from first principles.Keywords: metal insulator transition; Anderson localization; random disorder; typical medium theory; dynamical mean field theory; coherent potential approximation; dynamical cluster approximation; cellular dynamical mean field theory; cluster mean field theory
Real Space 3 Download Full Versionl
This will do 5 macro-cycles of global real-spacerefinement with rotamer, Ramachandran plot and C-beta deviationsrestraints enabled. If NCS is present it will be used as constraints withNCS groups found by the program automatically. Note: if map is used thenresolution needs to be provided.
debug = False Excessive output for debuggingmap_coefficients_label = None resolution = None write_initial_geo_file = True write_final_geo_file = False write_all_states = False write_pkl_stats = False model_format = *pdb *mmcif mask_and_he_map = False resolution_factor = 0.25 ncs_constraints = Auto refine_ncs_operators = Auto variable_rama_potential = False Switch between oldfield and emsley potentials during refinementweight = None real_space_target_exclude_selection = "element H or element D" Exclude selected atoms from real-space target calculationshow_statistics = True show_per_residue = True dry_run = False random_seed = 0 nproc = 1 gradients_method = fd linear quadratic *tricubic scattering_table = n_gaussian wk1995 it1992 *electron neutron Choices of scattering table for structure factors calculationsignore_symmetry_conflicts = False Ignore conflicting symmetry (normally use symmetry from map file)wrapping = Auto Wrap map outside of boundaries. Default is True for mtz file input, False otherwiseskip_map_model_overlap_check = False Skip map-model overlap checkabsolute_length_tolerance = 0.01 Length tolerance for comparing symmetriesabsolute_angle_tolerance = 0.01 Angle tolerance for comparing symmetriesjob_title = None Job title in PHENIX GUI, not used on command linerotamersfit = all *outliers_or_poormap outliers_and_poormap outliers poormap Fit side-chains regimestuneup = outliers outliers_and_poormap Switch remaining (after map fit) outliers to the nearest rotamerrestraintsenabled = True Use rotamer restraintssigma = Auto The smaller the value, the stronger the restraintstarget = max_distant min_distant exact_match fix_outliers Choice for the reference conformation to restrain torefinementrun = *minimization_global rigid_body *local_grid_search morphing simulated_annealing *adp *occupancy *nqh_flips adp_individual_isotropic = Auto Individual isotropic ADP refinementadp_individual_isotropic_restraints_weight = 1 Setting to 0 disables restraintsmorphing = every_macro_cycle once *first simulated_annealing = every_macro_cycle *once local_grid_search = every_macro_cycle once *last max_iterations = 100 macro_cycles = 5 target_bonds_rmsd = 0.01 target_angles_rmsd = 1 backbone_sample = None use_adp_restraints = True atom_radius = 3 do_ss_ideal = False do_ccd = False rigid_bodygroup = None amberParameters for using Amber in refinement.use_amber = False Use Amber for all the gradients in refinementtopology_file_name = None A topology file needed by Amber. Can be generated using phenix.AmberPrep.coordinate_file_name = None A coordinate file needed by Amber. Can be generated using phenix.AmberPrep.order_file_name = None A file that maps amber atom numbers to phenix atom numbers.wxc_factor = 1 restraint_wt = 0 restraintmask = "" reference_file_name = "" bellymask = "" If given, turn on belly in sanderqmmask = "" If given, turn on QM/MM with the given maskqmcharge = 0 Charge of the QM/MM regionnetcdf_trajectory_file_name = "" If given, turn on writing netcdf trajectoryprint_amber_energies = False Print details of Amber energies during refinementreference_modelenabled = False Restrains the dihedral angles to a high-resolution reference structure to reduce overfitting at low resolution. You will need to specify a reference PDB file (in the input list in the main window) to use this option.file = None use_starting_model_as_reference = False sigma = 1 limit = 15 hydrogens = False Include dihedrals with hydrogen atomsmain_chain = True Include dihedrals formed by main chain atomsside_chain = True Include dihedrals formed by side chain atomsfix_outliers = True Try to fix rotamer outliers in refined modelstrict_rotamer_matching = False Make sure that rotamers in refinement model matches those in reference model even when they are not outliersauto_shutoff_for_ncs = False Do not apply to parts of structure covered by NCS restraintssecondary_structure_only = False Only apply reference model restraints to secondary structure elements (helices and sheets)reference_groupreference = None selection = None file_name = None this is to used internally to disambiguate cases where multiple reference models contain the same chain ID. This normally does not need to be set by the usersearch_optionsSet of parameters for NCS search procedure. Some of them also used for filtering user-supplied ncs_group.exclude_selection = element H or element D or water Atoms selected by this selection will be excluded from the model before any NCS search and/or filtering procedures. There is no way atoms defined by this selection will be in NCS.chain_similarity_threshold = 0.85 Threshold for sequence similarity between matching chains. A smaller value may cause more chains to be grouped together and can lower the number of common residueschain_max_rmsd = 100 limit of rms difference between chains to be considered as copiesresidue_match_radius = 1000 Maximum allowed distance difference between pairs of matching atoms of two residuestry_shortcuts = False Try very quick check to speed up the search when chains are identical. If failed, regular search will be performed automatically.minimum_number_of_atoms_in_copy = 3 Do not create ncs groups where master and copies would contain less than specified amount of atomsvalidate_user_supplied_groups = True Enable validation of user-supplied ncs_group. Need to exercise a lot of caution turning this off. This option is for developers only.pdb_interpretationsort_atoms = True flip_symmetric_amino_acids = True superpose_ideal_ligand = *None all SF4 F3S DVT disable_uc_volume_vs_n_atoms_check = False allow_polymer_cross_special_position = False correct_hydrogens = True c_beta_restraints = True use_neutron_distances = False Use neutron X-H distances (which are longer than X-ray ones)disulfide_bond_exclusions_selection_string = None exclusion_distance_cutoff = 3 If SG of CYS forming SS bond is closer than this distance to an atom that it may coordinate then this SG is excluded from SS bond.link_distance_cutoff = 3 Length of link between the linked residuesdisulfide_distance_cutoff = 3 add_angle_and_dihedral_restraints_for_disulfides = True dihedral_function_type = *determined_by_sign_of_periodicity all_sinusoidal all_harmonic chir_volume_esd = 0.2 max_reasonable_bond_distance = 50 nonbonded_distance_cutoff = None default_vdw_distance = 1 min_vdw_distance = 1 nonbonded_buffer = 1 **EXPERIMENTAL, developers only**nonbonded_weight = 100 Weighting of nonbonded restraints term. By default, this will be set to 16 if explicit hydrogens are used (this was the default in earlier versions of Phenix), or 100 if hydrogens are missing.const_shrink_donor_acceptor = 0.6 **EXPERIMENTAL, developers only**vdw_1_4_factor = 0.8 min_distance_sym_equiv = 0.5 custom_nonbonded_symmetry_exclusions = None translate_cns_dna_rna_residue_names = None proceed_with_excessive_length_bonds = False restraints_librarycdl = True Use Conformation Dependent Library (CDL) for geometry restraintsmcl = True Use Metal Coordination Library (MCL) for tetrahedral Zn++ and iron-sulfur clusters SF4, FES, F3S, ...cis_pro_eh99 = True omega_cdl = False Use Omega Conformation Dependent Library (omega-CDL) for geometry restraintscdl_nucleotides = False Use RestraintsLib for DNA and RNA for geometry restraintscdl_nucleotides_esd = *phenix csd cdl_svl = False rdl = False rdl_selection = *all TRP hpdl = False secondary_structuress_by_chain = True Find secondary structure only within individual chains. Alternative is to allow H-bonds between chains. Can be much slower with ss_by_chain=False. If your model is complete use ss_by_chain=True. If your model is many fragments, use ss_by_chain=False.from_ca_conservative = False various parameters changed to make from_ca method more conservative, hopefully to closer resemble ksdssp.max_rmsd = 1 Maximum rmsd to consider two chains with identical sequences as the same for ss identificationuse_representative_chains = True Use a representative of all chains with the same sequence. Alternative is to examine each chain individually. Can be much slower with use_representative_of_chain=False if there are many symmetry copies. Ignored unless ss_by_chain is True.max_representative_chains = 100 Maximum number of representative chainsenabled = True Turn on secondary structure restraints (main switch)proteinenabled = True Turn on secondary structure restraints for proteinsearch_method = *ksdssp mmtbx_dssp from_ca cablam Particular method to search protein secondary structure.distance_ideal_n_o = 2.9 Target length for N-O hydrogen bonddistance_cut_n_o = 3.5 Hydrogen bond with length exceeding this value will not be establishedremove_outliers = True If true, h-bonds exceeding distance_cut_n_o length will not be establishedrestrain_hbond_angles = True helixserial_number = None helix_identifier = None enabled = True Restrain this particular helixselection = None helix_type = *alpha pi 3_10 unknown Type of helix, defaults to alpha. Only alpha, pi, and 3_10 helices are used for hydrogen-bond restraints.sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 Multiply sigmas for h-bond angles by this value. Original sigmas range from 5 to 10.angle_sigma_set = None Use this parameter to set sigmas for h-bond angles to a particular valuehbonddonor = None acceptor = None sheetenabled = True Restrain this particular sheetfirst_strand = None sheet_id = None sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 Multiply sigmas for h-bond angles by this value. Original sigmas range from 5 to 10.angle_sigma_set = None Use this parameter to set sigmas for h-bond angles to a particular valuestrandselection = None sense = parallel antiparallel *unknown bond_start_current = None bond_start_previous = None hbonddonor = None acceptor = None nucleic_acidenabled = True Turn on secondary structure restraints for nucleic acidshbond_distance_cutoff = 3.4 Hydrogen bonds with length exceeding this limit will not be establishedangle_between_bond_and_nucleobase_cutoff = 35 If angle between supposed hydrogen bond and basepair plane (defined by C4, C5, C6 atoms) is less than this value (in degrees), the bond will not be established.scale_bonds_sigma = 1 All sigmas for h-bond length will be multiplied by this number. The smaller number is tighter restraints.base_pairenabled = True Restraint this particular base-pairbase1 = None Selection string selecting at least one atom in the desired residuebase2 = None Selection string selecting at least one atom in the desired residuesaenger_class = 0 Type of base-pairingrestrain_planarity = False Apply planarity restraint to this base-pairplanarity_sigma = 0.176 restrain_hbonds = True Restrain hydrogen bonds length for this base-pairrestrain_hb_angles = True Restrain angles around hydrogen bonds for this base-pairrestrain_parallelity = True Apply parallelity restraint to this base-pairparallelity_target = 0 parallelity_sigma = 0.0335 stacking_pairenabled = True Restraint this particular base-pairbase1 = None Selection string selecting at least one atom in the desired residuebase2 = None Selection string selecting at least one atom in the desired residueangle = 0 sigma = 0.027 reference_coordinate_restraintsRestrains coordinates in Cartesian space to stay near their starting positions. This is intended for use in generating simulated annealing omit maps, to prevent refined atoms from collapsing in on the region missing atoms. For conserving geometry quality at low resolution, the more flexible reference model restraints should be used instead.enabled = False exclude_outliers = True selection = all sigma = 0.2 limit = 1 top_out = False automatic_linkinglink_all = False If True, bond restraints will be generated for any appropriate ligand-protein or ligand-nucleic acid covalent bonds. This includes sugars, amino acid modifications, and other prosthetic groups.link_none = False link_metals = Auto link_residues = False link_amino_acid_rna_dna = False link_carbohydrates = True link_ligands = True link_small_molecules = False metal_coordination_cutoff = 3.5 amino_acid_bond_cutoff = 1.9 inter_residue_bond_cutoff = 2.2 buffer_for_second_row_elements = 0.5 carbohydrate_bond_cutoff = 1.99 ligand_bond_cutoff = 1.99 small_molecule_bond_cutoff = 1.98 include_in_automatic_linkingselection_1 = None selection_2 = None bond_cutoff = 4.5 exclude_from_automatic_linkingselection_1 = None selection_2 = None apply_cis_trans_specificationcis_trans_mod = cis *trans residue_selection = None Residues containing C-alpha atom of omega dihedralapply_cif_restraintsrestraints_file_name = None residue_selection = None apply_cif_modificationdata_mod = None residue_selection = None apply_cif_linkdata_link = None residue_selection_1 = None residue_selection_2 = None peptide_linkramachandran_restraints = False !!! OBSOLETED. Kept for backward compatibility only !!! Restrains peptide backbone to fall within allowed regions of Ramachandran plot. Although it does not eliminate outliers, it can significantly improve the percent favored and percent outliers at low resolution. Probably not useful (and maybe even harmful) at resolutions much higher than 3.5A.cis_threshold = 45 apply_all_trans = False discard_omega = False discard_psi_phi = True apply_peptide_plane = False omega_esd_override_value = None rama_weight = 1 scale_allowed = 1 rama_potential = *oldfield emsley rama_selection = None Selection of part of the model for which Ramachandran restraints will be set up.restrain_rama_outliers = True Apply restraints to Ramachandran outliersrestrain_rama_allowed = True Apply restraints to residues in allowed region on Ramachandran plotrestrain_allowed_outliers_with_emsley = False In case of restrain_rama_outliers=True and/or restrain_rama_allowed=True still restrain these residues with emsley. Make sense only in case of using oldfield potential.oldfieldesd = 10 weight_scale = 1 dist_weight_max = 10 weight = None plot_cutoff = 0.027 ramachandran_plot_restraintsenabled = True favored = *oldfield emsley emsley8k phi_psi_2 allowed = *oldfield emsley emsley8k phi_psi_2 outlier = *oldfield emsley emsley8k phi_psi_2 selection = None Selection of part of the model for which Ramachandran restraints will be set up.inject_emsley8k_into_oldfield_favored = True Backdoor to disable temporary dirty hack to use botholdfieldweight = 0 Direct weight value. If 0 the weight will be calculated as following: (w, op.esd, op.dist_weight_max, 2.0, op.weight_scale) 1 / esd^2 * max(2.0, min(current_distance_to_allowed, dist_weight_max)) * weight_scale max(2.0, current_distance_to_allowed) 1 / esd^2 * weight_scale * max(distance_to_allowed_cutoff, current_distance_to_allowed) weight_scale(=0.01) * max(distance_weight_min(=2.), min(distance_weight_max(=10.), current_distance_to_allowed))weight_scale = 0.01 distance_weight_min = 2 minimum coefficient when scaling depending on how far the residue is from allowed region.distance_weight_max = 10 maximum coefficient when scaling depending on how far the residue is from allowed region.plot_cutoff = 0.027 emsleyweight = 1 scale_allowed = 1 emsley8kweight_favored = 5 weight_allowed = 10 weight_outlier = 10 phi_psi_2favored_strategy = *closest highest_probability random weighted_random allowed_strategy = *closest highest_probability random weighted_random outlier_strategy = *closest highest_probability random weighted_random rna_sugar_pucker_analysisbond_min_distance = 1.2 bond_max_distance = 1.8 epsilon_range_min = 155 epsilon_range_max = 310 delta_range_2p_min = 129 delta_range_2p_max = 162 delta_range_3p_min = 65 delta_range_3p_max = 104 p_distance_c1p_outbound_line_2p_max = 2.9 o3p_distance_c1p_outbound_line_2p_max = 2.4 bond_detection_distance_tolerance = 0.5 show_histogram_slotsbond_lengths = 5 nonbonded_interaction_distances = 5 bond_angle_deviations_from_ideal = 5 dihedral_angle_deviations_from_ideal = 5 chiral_volume_deviations_from_ideal = 5 show_max_itemsnot_linked = 5 bond_restraints_sorted_by_residual = 5 nonbonded_interactions_sorted_by_model_distance = 5 bond_angle_restraints_sorted_by_residual = 5 dihedral_angle_restraints_sorted_by_residual = 3 chirality_restraints_sorted_by_residual = 3 planarity_restraints_sorted_by_residual = 3 residues_with_excluded_nonbonded_symmetry_interactions = 12 fatal_problem_max_lines = 10 ncs_groupThe definition of one NCS group. Note, that almost always in refinement programs they will be checked and filtered if needed.reference = None Residue selection string for the complete master NCS copyselection = None Residue selection string for each NCS copy loca