|edat = <energy_data>||objective function parameters|
|file = <str:1>||'default'||root of output filename(s)|
|accessibility_type = <int:1>||8||type of solvent accessibility: 1-10|
|surftyp = <int:1>||1||Surface Type for accessibility calculations 1= contact; 2=surface|
|psa_integration_step = <float:1>||0.1||integration step for WRITE_DATA|
|probe_radius = <float:1>||1.4||probe_radius for WRITE_DATA|
|neighbor_cutoff = <float:1>||6.0||for defining atom-atom contacts in WRITE_DATA|
|output = <str:1>||'LONG'||what to calculate and write out: 'ALL' | 'PSA' | 'ATOMIC_SOL' | 'NGH' | 'DIH' | 'SSM' | 'CRV' | 'CAV' | 'CROSS-SECTIONS' | 'HBONDS'|
This command writes the selected types of data about the MODEL to a corresponding file. The last such property is also assigned to the B field of the model (this can later be written out with model.write() to a PDB file, where it appears as the temperature factor). The root of the output filenames is given by the file variable.
Properties can be chosen from the following list: atomic or residue accessibility, dihedral type accessibility_type (from 1 to 9 for , , , , , , , , and ; where is the virtual dihedral angle between four successive atoms), number of residue neighbors, the secondary structure type, and the local mainchain curvature. For accessibility, when output contains ATOMIC_SOL, atomic accessibilities in Å are assigned to B , otherwise residue accessibility of type accessibility_type (from 1 to 10, for the columns in the .psa file) is assigned. If surftyp is 1, contact accessibility is calculated; if 2, surface accessibility is returned.
The data to be calculated are specified by concatenating the corresponding keywords in the output variable:
Kinking residues have both DRMS and maximal distance difference beyond their respective cutoffs ( , ). The actual single kink residue separating the two new segments of the same type is the central kinking residue. Note: we are assuming that there are no multiple kinks within one contiguous segment of residues of the same secondary structure type. The kink residue type is .