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

Output:

molpdf

Description:

This command assesses the quality of the model using the GA341 method method [Melo et al., 2002]. 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.)

Example: examples/commands/assess_ga341.py

# Example for: model.assess_ga341()

env = environ()

# Read a model previously generated by Modeller's automodel class
mdl = model(env, file='../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()