WRITE_DATA -- write derivative MODEL data

FILE = <string:1>	'default'	root of output filename(s)
ACCESSIBILITY_TYPE = <integer:1>	8	type of solvent accessibility: 1-10
SURFTYP = <integer:1>	1	Surface Type for accessibility calculations 1= contact; 2=surface
TOPOLOGY_MODEL = <integer:1>	3	selects topology library: 1-10
RADII_FACTOR = <real:1>	0.82	factor for van der Waals radii
PSA_INTEGRATION_STEP = <real:1>	0.1	integration step for WRITE_DATA
PROBE_RADIUS = <real:1>	1.4	probe_radius for WRITE_DATA
NUMBER_OF_STEPS = <integer:1>	1	for calculating cavity volume
GRID_UNIT = <real:1>	1	grid size for cavities calculation in WRITE_DATA
ACCURACY_BORDER = <logical:1>	off	whether or not the closure on the surface accepts diagonal cords
RCUTL = <real:1>	5.0	Radius of cut-off for a long sphere of atoms
RCUTP = <real:1>	3.0	Radius of cut-off for a short sphere of atoms
ORIENT = <logical:1>	off	whether or not to orient structure before volume calculation in WRITE_DATA
OUTPUT = <string:1>	'LONG'	what to calculate and write out: 'ALL' | 'PSA' | 'ATOMIC_SOL' | 'NGH' | 'DIH' | 'SSM' | 'CRV' | 'CAV' | 'CROSS-SECTIONS'

Requirements:

topology file & TOPOLOGY_MODEL

Description:

This command writes the selected types of data about the MODEL to a corresponding file and to the `fourth' column of the model. The root of the output filenames is given by the FILE variable. In addition to the output files, the $B_{\mbox{iso}}$ field of the model (`fourth column' in the PDB file) will be assigned the last selected property from the following list: atomic or residue accessibility, dihedral type ACCESSIBILITY_TYPE (from 1 to 9 for $\alpha$, $\Phi$, $\Psi$, $\omega$, $\chi_1$, $\chi_2$, $\chi_3$, $\chi_4$, and $\chi_5$; where $\alpha$ is the virtual dihedral angle between four successive ${C}_\alpha$ atoms), number of residue neighbors, the secondary structure type, and the local mainchain curvature. For accessibility, when OUTPUT contains ATOMIC_SOL, atomic accessibilities in $\mbox{\AA}^2$ are assigned to $B_{\mbox{iso}}$, 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:

• 'ALL': All types of data are written to the corresponding files.

• 'PSA': The atomic and residue solvent accessibilities are written to the .sol and .psa files, respectively. The algorithm for the solvent contact areas is described in [Richmond & Richards, 1978]. The normalization for the fractional areas is carried out as described in [Hubbard & Blundell, 1987], with the normalization factors courtesy of Simon Hubbard (personal communication). The single reference is [Šali & Overington, 1994]. Accessibilities are calculated with scaled radii from the $MODELS_LIB library, as specified by TOPOLOGY_MODEL. The radii are scaled by RADII_FACTOR, which should usually be set to 1.

• 'CAV': The protein and internal cavity volumes are written out. The calculation on a grid is used. The grid unit is specified by GRID_UNIT in angstroms (say 1.4). The radii are scaled by RADII_FACTOR, which should usually be set to 1. The cross-sections are written to file FILE.cav when OUTPUT contains CROSS-SECTIONS. The NUMBER_OF_STEPS is the number of small shifts along x, y, and z that are used in the averaging of the protein and cavity volumes with respect to small changes in the relative position of the protein and the grid; the total number of calculations is therefore equal to the third power of NUMBER_OF_STEPS. If ORIENT is on, the structure is oriented before the volume calculation such that the moment of inertia are parallel to the x, y, and z coordinate axes (this orientation minimizes the size of the grid). However, the coordinates of the MODEL are not changed upon exit from this routine (you need to use ORIENT_MODEL to change the orientation of the MODEL).

• 'NGH': Residue neighbors of each residue are listed to a .ngh file. The MODELLER definition of a residue-residue contact used in restraints derivation is applied [Šali & Blundell, 1993]: Any pair of residues that has any pair of atoms within 6Å of each other are in contact.

• 'DIH': All the dihedral angle types defined in the $RESDIH_LIB library (virtual ${C}_\alpha$, mainchain, and sidechain dihedral angles) are written to a .dih file.

• 'SSM': Secondary structure assignments are written to a .ssm file. The algorithm for secondary structure assignment depends on the ${C}_\alpha$ positions only and is based on the distance matrix idea described in [Richards & Kundrot, 1988]. For each secondary structure type, a `library' ${C}_\alpha$ distance matrix was calculated by averaging distance matrices for several secondary structure segments from a few high resolution protein structures. Program DSSP was used to assign these secondary structure segments [Kabsch & Sander, 1983]. Outlier distances were omitted from the averaging. Currently, there are only two matrices: one for the $\alpha$-helix (secondary structure type 2) and one for the $\beta$-strand (type 1). The algorithm for secondary structure assignment is as follows:
  1. For each secondary structure type (begin with a helix, which can thus overwrite parts of strand if they overlap):
     • Define the degree of the current secondary structure fit for each ${C}_\alpha$ atom by DRMS deviation ($P_1$) and maximal distance difference ($P_2$) obtained by comparing the library distance matrix with the distance matrix for a segment starting at the given ${C}_\alpha$ position;

     • Assign the current secondary structure type to all ${C}_\alpha$'s in all segments whose DRMS deviation and maximal distance difference are less than some cutoffs ($P_1<cut_1$, $P_1<cut_2$) and are not already assigned to `earlier' secondary structure types;

  2. Split kinked contiguous segments of the same type into separate segments:

     Kinking residues have both DRMS and maximal distance difference beyond their respective cutoffs ($P_1>cut_3$, $P_2>cut_4$). 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 $-2$.

  3. If the current secondary structure type is $\beta$-strand: Eliminate those runs of strand residues that are not close enough to other strand residues separated by at least two other residues: $P_3$ is minimal distance to a non-neighboring residue of the strand type ($P_3 < cut_3$). Currently, only one pass of this elimination is done, but could be repeated until self-consistency.

  4. Eliminate those segments that are shorter than the cutoff ($cut_6$) length (e.g., 5 or 6).

  5. Remove the isolated kinking residues (those that occur on their own or begin or end a segment).

• 'CRV': Local mainchain curvatures are written to a .crv file. Local mainchain curvature at residue $i$ is defined as the angle between the least-squares lines through ${C}_\alpha$ atoms $i-3$ to $i$ and $i$ to $i+3$.

Example:

# Example for: WRITE_DATA

# This will calculate solvent accessibility, dihedral angles, and 
# residue-residue neighbors for a structure in the PDB file.

SET OUTPUT_CONTROL = 1 1 1 1 1

# Get topology library for radii and the model without waters and HETATMs:
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
SET HETATM_IO = off, WATER_IO = off
READ_MODEL FILE = '1fas'

# Calculate residue solvent accessibilities, dihedral angles, and 
# residue-residue neighbors:
SET RADII_FACTOR = 1.0 # The default is 0.82 (for soft-sphere restraints)
WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV'