vars: a b c alpha beta gamma info: Unit cell dimensions. The lengths of the unit cell axes (a, b and c) are in Angstroms. The angles between axes (alpha, beta, gamma) are in degrees. # vars: anom_library info: A file which contains the f' and f'' values for anomalous scattering. There are library file supplied with CNS for both copper and molybdenum wavelengths (CNS_XRAYLIB:anom_cu.lib CNS_XRAYLIB:anom_mo.lib). # vars: bscale info: Method for overall B-value correction of the data. The current model and the observed data will compared and used to derive an overall correction. # vars: coordinate_infile coordinate_infile_\d+ \w+_coordinate_infile info: Input CNS coordinate file. This file contains atomic coordinates in PDB type format. # vars: fft_memory info: Memory (in words) allocated for fast Fourier transform (FFT). If a negative value is used the memory space will be automatically determined. # vars: high_res info: Highest resolution limit (ie. minimum Bragg spacing) for calculations. # vars: low_res_bscale info: Lowest resolution limit for data used in calculation of overall B-value correction. # vars: low_res info: Lowest resolution limit (ie. maximum Bragg spacing) for calculations. # vars: obs_f info: Reciprocal space array defined in the reflection file which contains the observed diffraction amplitudes. # vars: obs_fom info: Reciprocal space array defined in the reflection file which contains the observed figures-of-merit (FOM) from experimental phasing. # vars: obs_i info: Reciprocal space array defined in the reflection file which contains the observed diffraction intensities. # vars: obs_pa obs_pb obs_pc obs_pd p[a-d]_\d+ p[a-d]_in info: Reciprocal space arrays defined in the reflection file which contain a phase probability distribution in the form of Hendrickson-Lattman coefficients. # vars: p[a-d]_out info: Name for output reciprocal space arrays which contain a phase probability distribution in the form of Hendrickson-Lattman coefficients. # vars: obs_phase info: Reciprocal space array defined in the reflection file which contains the observed centroid phases from experimental phasing. # vars: obs_rms f_rms info: RMS cutoff for outlier rejection. # vars: obs_sigf f_cut info: Reciprocal space array defined in the reflection file which contains the sigma values for the observed diffraction amplitudes. # vars: obs_sigi info: Reciprocal space array defined in the reflection file which contains the sigma values for the observed diffraction intensities. # vars: obs_type info: Which experimental observations (amplitudes or intensities) to use for outlier rejection. # vars: obs_w info: Reciprocal space array defined in the reflection file which contains weights for each observation. # vars: coordinate_outfile output_coor info: Output coordinate file in PDB format. # vars: parameter_infile_\d+ par.\d+ par_\d+ info: CNS parameter file. The geometric parameters for bonds, angles, impropers and dihedrals are defined in this file. Also defined are the nonbonded parameters for each atom type. There are parameter files available for crystallographic refinement: There are parameter files available for NMR structure determination: # vars: reflection_outfile_\d+ reflection_infile_\d+ reflection_infile info: Reflection file. This free format file contains initial definiations of the data object present. Entries are per reflection and are identified by the reciprocal lattice index (HKL). Each reflection has values for the data objects defined at the beginning of the file: 
 NREFlection=      8721
 ANOMalous=FALSe { equiv. to HERMitian=TRUE}
 DECLare NAME=FOBS         DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=SIGMA        DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=TEST         DOMAin=RECIprocal   TYPE=INTE END
 INDE     4    1    0 FOBS=    64.207 SIGMA=     3.626 TEST=    0
 INDE     0    0    3 FOBS=  1047.380 SIGMA=    18.630 TEST=    0

The header for a file with experimental phase information should look like this:

 NREFlection=           1400
 ANOMalous=TRUE { equiv. to HERMitian=FALSe}
 DECLare NAME=FOBS        DOMAin=RECIprocal   TYPE=COMP END
 DECLare NAME=SIGMA       DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=PA          DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=PB          DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=PC          DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=PD          DOMAin=RECIprocal   TYPE=REAL END
 GROUp TYPE=HL
   OBJEct=PA
   OBJEct=PB
   OBJEct=PC
   OBJEct=PD
 END
 INDE     0    4    2 FOBS=     677.8       0.0 SIGMA=     19.40
                      PA=    -0.486 PB=     0.000 PC=     0.000 PD=     0.000
# vars: sg info: Space group. This describes the symmetry of the crystal. This uses the the standard International Tables nomenclature, with subscripts denoted by parentheses. eg. P2(1)2(1)2(1). Both hexogonal (the default) and rhombohedral setting are available for rhombohedral space groups. The latter are obtained by appending R to the spacegroup name (for example, R3R is the rhombohedral setting for R3). # vars: sigma_cut info: Sigma cutoff value for rejection of weak data. This should not be used without a good reason, even weak data are useful in refinement. # vars: structure_infile structure_file \w+_structure_infile structure_infile_\d+ struct.\d+ info: CNS molecular structure file. This contains the information describing the topology of the molecule, ie. which atoms form bonds, angles, dihedrals. The molecular topology file should not be edited manually. # vars: psf_infile psf_outfile info: Molecular structure file in X-PLOR compatible PSF format. This contains information describing the topology of the molecule, ie. which atoms form bonds, angles, dihedrals. This file should not be edited manually. # vars: test_flag info: The value of the test set flag that will be used for cross-validation. # vars: test_set info: Reciprocal space array defined in the reflection file which contains the test set flag. # vars: output_root output_root_\d+ info: Root name for the output files that are written by the task file. # vars: mask_infile \w+_mask_infile \w+_mask_infile_\d+ info: Mask file in compressed O format. # vars: restraints_infile info: A file which defines additional restraints for the system. This would usually be restraints that maintain the geometry of DNA/RNA. See the example file auxiliary/dna-rna_restraints.def. # vars: ncs_infile info: File containing the definition of the non-crystallographic symmetry (NCS). See file auxiliary/ncs.def. # vars: list_outfile info: Listing file. # vars: atom_select atom_select_\d+ atom_select.\d+ info: Atom selection identifying atoms which will included in the calculations. # vars: write_map info: Write electron density map. # vars: atom_main info: Atom selection identifying atoms which are to be considered as mainchain atoms for the purposes of individual B-value refinement. # vars: bulk_sol info: Should a bulk-solvent correction be applied. # vars: map_format info: Format of output electron density map. Choices are CNS format or EZD format. The CNS map files can be read into MAPMAN using the X-PLOR format. The EZD map files can be read into MAPMAN using the NEWEZD format. # vars: map_mode info: Determines the extent of the output electron density map. # vars: sol_b sol_k info: Parameters for the bulk solvent correction. # vars: target_bins info: Number of equal volume reciprocal space bins to use in the calculation of the crystallographic target function. # vars: xmax xmin ymax ymin zmax zmin info: Limits of electron density map in orthogonal Angstroms or fractional coordinates (depending on the map mode). # vars: asig_main info: Target sigma for distribution of B-values for mainchain atoms which form angles. # vars: asig_side info: Target sigma for distribution of B-values for sidechain atoms which form angles. # vars: bsig_main info: Target sigma for distribution of B-values for mainchain atoms which form bonds. # vars: bsig_side info: Target sigma for distribution of B-values for sidechain atoms which form bonds. # vars: minimize_nstep info: Number of steps of conjugate gradient energy minimization. # vars: num_cycles info: Number of cycles of optimization to be performed. # vars: pdb_o_format info: Write the output PDB file in a format more friendly for O (chain identifiers are written and the CRYST card). # vars: reftarget info: Crystallographic target function. # vars: structure_outfile info: Output molecular topology file. # vars: atom_fixed info: Atom selection identifying atoms which are to remain fixed during refinement. # vars: atom_harm info: Atom selection identifying atoms which are to be harmonically restrained during refinement. # vars: atom_map info: Atom selection identifying atoms around which the electron density map will be written out. # vars: atom_rigid info: Atom selection identifying atoms which will be treated as rigid bodies in torsion angle dynamics refinement. # vars: bfactor_nstep info: Number of steps of conjugate gradient B-factor minimization. # vars: bins info: The number of equal volume reciprocal space resolution bins. # vars: constant_steps info: Number of steps of molecular dynamics to be performed at constant temperature. # vars: cool_rate info: Drop in temperature (K) per cycle of dynamics. This determines the rate of slowcooling during simulated annealing. Values of from 25 to 50 are appropriate. # vars: k_harmonic info: Force constant (kcal/mol/A^2) for harmonically restrained atoms. # vars: low_res_wilson info: Low resolution limit in Å for calculation of the Wilson B-value. This should be numerically less than 3Å (at resolutions worse than this the Wilson B-value cannot be accurately estimated). # vars: map_cushion info: Cushion in Angstroms around the molecule, used when writing maps. # vars: map_scale info: The map will be scaled by the RMS of the map. Scaled maps will be written out in units of sigma. # vars: map_type info: What type of map to make. # vars: mask_outfile info: Output mask in compressed O format. # vars: md_scheme info: Simulated annealing strategy. Either slowcooling or constant temperature. # vars: md_type info: Molecular dynamics algorithm. Either Cartesian (restrained) dynamics or torsion angle (constrained) dynamics. # vars: num_trials info: Number of independent simulated annealing trials to be performed. # vars: peak_search info: Perform peak searching on resulting map. # vars: reflection_outfile info: Output reflection file. # vars: reset_b info: If positive reset all B-values to this value prior to calculations. # vars: rigid_nstep info: Number of steps of conjugate gradient rigid-body minimization. # vars: seed info: Starting random number seed. # vars: temperature info: Molecular dynamics temperature. For the slowcooing protocol this is the starting temperature. For the constant temperature protocol this is the temperature for the entire run. # vars: torsion_maxbond info: Maximum number of bonds to an atom. # vars: torsion_maxchain info: Maximum number of chains. # vars: torsion_maxlength info: Maximum length of an unbranched chain. # vars: torsion_maxtree info: Maximum number of trees. # vars: u info: Coefficient for observed diffraction data in map calculation. # vars: v info: Coefficient for calculated diffraction data in map calculation. # vars: r_group_\d+ info: For rigid body refinement this is an atom selection identifying atoms which form rigid bodies. The rotation and translation of each group of atoms will be refined. # vars: conf_\d+ info: Atoms selection identifying atoms in an alternate conformation. # vars: anneal info: Perform simulated annealing. # vars: reset_q info: If positive reset all occupancies to this value prior to calculations. # vars: grid info: Resolution of the grid for maps, relative to the high resolution limit in reciprocal space (e.g. of the diffraction data). In general, the resolution of the grid for maps is 1/3 to 1/4 of the high resolution in reciprocal space. For example, given grid_res=0.333, if the high resolution limit of the diffraction data is 3Å, the grid spacing of the map is about 1Å in each dimension. # vars: sitedatabase_infile(\.\d+)? sitedatabase_outfile(\.\d+)? info: CNS site database (SDB) file. This file contains atomic coordinates, B-factors, occupancies, derivative names, and chemical types. Atoms can be grouped by assigning a common group label. Grouped atoms are treated as rigid bodies in refinement. Useful task files for the manipulation of SDB files are generate_sdb.inp, sdb_manipulate.inp, delete_sites.inp, sdb_split.inp, sdb_to_pdb.inp, sdb_to_sdb.inp, flip_sites.inp, and shift_sites.inp. # vars: map_outfile info: Output electron density map in the selected format. # vars: merge_inout info: Merge original input information with newly generated information prior to writing. In general it is best to not merge the data in order to reduce the size of data files. #