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model.write_data() -- write derivative MODEL data

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'

Requirements:
topology file

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:

Example: examples/commands/write_data.py


# Example for: model.write_data()

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

log.verbose()

# Get topology library for radii and the model without waters and HETATMs:
env = environ()
env.io.hetatm = False
env.io.water = False

env.libs.topology.read(file='$(LIB)/top_heav.lib')
mdl = model(env, file='1fas')

# Calculate residue solvent accessibilities, dihedral angles, and 
# residue-residue neighbors:
myedat = energy_data()
myedat.radii_factor = 1.0 # The default is 0.82 (for soft-sphere restraints)
mdl.write_data(file='1fas', edat=myedat, output='PSA DIH NGH SSM CRV')


next up previous contents index
Next: model.write_pdb_xref() write Up: The model class: handling Previous: model.rotate() rotate   Contents   Index
Ben Webb 2005-04-21