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[modeller_usage] grid_search and hetatm

Dear Modellers

I am fitting a protein with cofactors in a cryo-em density using grid_search. It works but the fitted structure does’t include anymore the HETATM fields with the cofactors.

My input looks

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

den.grid_search(em_density_format='MRC', num_structures=1,
                em_pdb_name=struct, chains_num=[1],
                start_type='SPECIFIC', number_of_steps=1000,
                angular_step_size=30., temperature=150.,
                best_docked_models=1, translate_type='RANDOM',

Is this something that is not supported or I am doing something wrong?


Department of Biosciences
University of Milano
Via Celoria 26 - 20133 Milano, Italy

www: sites.unimi.it/camilloni