model.write_data() -- write derivative MODEL data

write_data(output, file, surftyp=1, neighbor_cutoff=6.0, accessibility_type=8, probe_radius=1.4, psa_integration_step=0.1, dnr_accpt_lib='$LIB/donor_acceptor.lib', edat=None)

Requirements:

topology file

This command writes the selected types of data about the MODEL to a corresponding file. The last such property (from the list below) is also assigned to the B${}_{iso}$ 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.

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], and can be tuned by changing the probe_radius and psa_integration_step parameters. 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.submodel. The radii are scaled by energy_data.radii_factor, which should usually be set to 1. If output also contains ATOMIC_SOL, atomic accessibilities in $\AA^2$ are assigned to B${}_{iso}$ , 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.

• '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 neighbor_cutoff Å of each other are in contact.

• 'DIH': All the dihedral angle types defined in the $RESDIH_LIB library (mainchain, sidechain, and the virtual dihedral between four successive ${C}_\alpha$ atoms, starting with the previous residue) are written to a .dih file. One column from this file, as selected by accessibility_type, is also assigned to B${}_{iso}$ .

• '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 assigned to the B${}_{iso}$ field. 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 $i+3$ .

• 'HBONDS': Hydrogen bonds between amino acid residues are written to a .hbnds file. A list of donors and acceptors in the 20 naturally occurring amino acids, specified by dnr_accpt_lib, is utilized in the computation of H-bonds. Hydrogen bonds are reported if the donor - acceptor distance is between 2.5 and 3.5Å and the donor-acceptor-acceptor antecedent angle is larger than 120 degrees. The model's B${}_{iso}$ field is not changed by this property.