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 & Šali, 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.

When using automodel or loopmodel, automatic GA341 assessment of each model can be requested by adding assess.GA341 to automodel.assess_methods or loopmodel.loop.assess_methods respectively.

Example: examples/assessment/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()