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.
# 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()