model.assess_ga341() -- assess a model with the GA341 method

assess_ga341()

Output:

(score, compactness, e_native_pair, e_native_surf, e_native_comb, z_pair, z_surf, z_comb)

This command assesses the quality of the model using the GA341 method method [Melo et al., 2002,John & Š ali, 2003]. The method uses the percentage sequence identity between the template and the model as a parameter. MODELLER-produced PDB files contain this information in a 'REMARK'; in the case of other PDB files, you should supply this by setting model.seq_id.

If the model contains multiple chains, only the first is evaluated by this method; if you wish to evaluate the model in a different chain, you should write out that single chain into a new model first. (The method was parameterized for use with single-chain proteins, so its use for multi-chain models is not recommended.)

Only standard amino acids are assessed by this command. A ModellerError exception will be raised if the model contains no standard amino acids.

Example: examples/commands/assess_ga341.py

# Example for: model.assess_ga341()

from modeller import *
from modeller.scripts import complete_pdb

env = environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

# Read a model previously generated by Modeller's automodel class
mdl = complete_pdb(env, '../atom_files/1fdx.B99990001.pdb')

# Set template-model sequence identity. (Not needed in this case, since
# this is written by Modeller into the .pdb file.)
mdl.seq_id = 37.037

score = mdl.assess_ga341()