############################################################################### # Parameter names matched in common.idb: # a # b # c # alpha # beta # gamma # coordinate_infile # grid # high_res # low_res # obs_f # obs_i # obs_pa # obs_pb # obs_pc # obs_pd # obs_sigf # obs_sigi # reflection_infile_\d+ # sg # test_flag # test_set # output_root # write_map # map_mode # xmax # xmin # ymax # ymin # zmax # zmin # minimize_nstep # num_cycles # reftarget # bfactor_nstep # map_type # anneal ############################################################################### # vars: bases_planar info: Atom selection defining bases whose planarity will be restrained. The selection of the appropriate atoms which form a plane is performed automatically. This selection should only include nucleotides, selection of other atoms may lead to inappropriate restraints for non-nucleotide residues. # vars: pucker_\d+ info: Atom selection defining residues whose ribose sugar pucker will be restrained. # vars: form_\d+ info: String defining the ribose sugar pucker for the selected atoms. Puckers can be either A-form or B-form DNA/RNA or user defined. Puckers are maintained by the application of dihedral angle restraints in the ribose ring. The restraints for A-form and B-form are:
FormNu2Nu3Nu4
A37.053-155.59144.26
B-34.90-86.40106.4
# vars: dihedral_nu2_\d+ info: User defined dihedral angle restraint for the Nu2 dihedral in the selected ribose rings. # vars: dihedral_nu3_\d+ info: User defined dihedral angle restraint for the Nu3 dihedral in the selected ribose rings. # vars: dihedral_nu4_\d+ info: User defined dihedral angle restraint for the Nu4 dihedral in the selected ribose rings. # vars: base_a_\d+ info: Atom selection defining the first base in a Watson-Crick base pair. Only one base should be selected. Watson-Crick base pairing is maintained by the use of distance restraints between the non-hydrogen atoms involved in Watson-Crick hydrogen bonding. # vars: base_b_\d+ info: Atom selection defining the second base in a Watson-Crick base pair. Only one base should be selected. Watson-Crick base pairing is maintained by the use of distance restraints between the non-hydrogen atoms involved in Watson-Crick hydrogen bonding. # vars: site.action_\d+ info: String defining how this heavy atom site will be treated. Sites can be marked for inclusion in heavy atom calculations either as refined or fixed. Alternatively sites can be marked as ignored. The latter is useful if incorrect sites are present in a site database file which are to be excluded from subsequent calculations. # vars: site.segid_\d+ info: String defining the derivative name, this can be a maximum of 4 characters. In MAD refinement all active sites in a site database file are used (unwanted sites should be marked as ignored). In isomorphous replacement refinement the derivative name given in the task file will be matched against the derivative names in the input site database file. # vars: site.type_\d+ info: String defining the chemical type of the heavy atom site. This is used to obtain atomic scattering factors for the heavy atom. The chemical type should match the chemical types defined in the scattering libraries (see CNS_XRAYLIB:scatter.lib). The 2 letter atomic symbol is usually appropriate. # vars: site.x_\d+ info: X coordinate of heavy atom in orthogonal Å (using the PDB convention). # vars: site.y_\d+ info: Y coordinate of heavy atom in orthogonal Å (using the PDB convention). # vars: site.z_\d+ info: Z coordinate of heavy atom in orthogonal Å (using the PDB convention). # vars: site.b_\d+ info: B-value of heavy atom in Å^2. # vars: site.q_\d+ info: Occupancy of heavy atom. # vars: site.g_\d+ info: Group identifier (string). Heavy atom sites with the same group identifier will be refined as a rigid body (coordinates, B-values, occupancies and f'/f''). This can be used to refine heavy atom clusters as a rigid body. The group identifier should be a maximum of 4 characters in length. Usually the group identifier is left blank, in which case all heavy atoms will be refined individually. # vars: ncs_type info: Defines the type of non-crystallographic symmetry (NCS) to be applied. There are two choices, either strict NCS (NCS constraints) or restrained NCS. In the strict case the model contains only the basic protomer and the NCS defines all the operations that generate the complete molecular assembly. The NCS operators are applied to all atoms in the input model. In the restrained case the model contains the full molecular assembly and restraints are defined between molecules in the asymmetric unit. The restraints maintain a similar conformation between NCS related molecules. The NCS operators relating the molecules are not defined, and are thus not fixed during refinement. # vars: skew_use info: Flag indicating whether a skew matrix is to be used for strict NCS. # vars: skew_matrix info: CNS matrix defining the rotational component of the skew operator. The matrix format is: 
( a11 a12 a13 )
( a21 a22 a23 )
( a31 a32 a33 )
# vars: skew_vector info: CNS vector defining the translational component of the skew operator. The vector format is: 
( a1 a2 a3 )
# vars: ncs_op_\d+ info: Flag indicating whether this strict NCS operator should be used. This operator will be used to generate the full asymmetric unit for the calculation of structure factors and nonbonded interactions between NCS related molecules within the asymmetric unit. Crystallographic interactions between the input model and NCS related molecules are not calculated. # vars: ncs_matrix_\d+ info: CNS matrix defining the rotational component of the NCS operator. The matrix format is: 
( a11 a12 a13 )
( a21 a22 a23 )
( a31 a32 a33 )
# vars: ncs_vector_\d+ info: CNS vector defining the translational component of the NCS operator. The vector format is in orthogonal Å: 
( a1 a2 a3 )
# vars: nb_ncs_op_\d+ info: Flag indicating whether this strict nonbonded NCS operator should be used. This operator will be used to generate additional nonbonded interactions between NCS related molecules. These operators are usually used to define the full crystallographic environment around the input model. These can be used to replace the missing crystallographic interactions between the input model and NCS related molecules. # vars: nb_ncs_matrix_\d+ info: CNS matrix defining the rotational component of the nonbonded NCS operator. The matrix format is: 
( a11 a12 a13 )
( a21 a22 a23 )
( a31 a32 a33 )
# vars: nb_ncs_vector_\d+ info: CNS vector defining the translational component of the nonbonded NCS operator. The vector format is in orthogonal Å: 
( a1 a2 a3 )
# vars: group.\d+.weight info: The restraint weight in kcal/mole/Å^2 for this NCS group. Each NCS group defines a set of molecules, domains or atoms that are related by NCS symmetry. The restraint weight determines how tightly the NCS is restrained. A weight of 300 to 500 will result in very tight restraints (the NCS related atoms will superimpose with a low RMSD). A restraint weight of 10 will result in very weak restraints (the NCS related atoms may superimpose with a high RMSD). A high weight should be used initially, this weight can then be decreased and the free R-value monitored to determine the optimal weight. # vars: group.\d+.sigb info: The target deviation in Å^2 for B-values between NCS related atoms. This is used in restrained B-value refinement and determines the deviation from the average B-value for NCS related atoms. A value of 2 is suggested by default. NCS related molecules which show large differences in overall B-values may require a increased target deviation. # vars: group.\d+.equiv.\d+ info: Atom selection specifying a set of atoms who are related to the other atom sets by non-crystallographic symmetry. The first selected atom set is used as the reference for superimposing molecules in order to calculate the NCS restraint energy term and forces. This does not imply that the equivalent atoms will be restrainted to the reference. Instead all equivalent sets, including the reference, will be restrained to the average of all sets. # vars: map_coeff_\d+ info: Coefficients for the output electron density map. The type of map (Sigma-A weighted, phase combined etc) is set elsewhere. The possible options are: #