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',

                em_fit_output_file='modem.log’)

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

Best,

Carlo

_______

Department of Biosciences

University of Milano

Via Celoria 26 - 20133 Milano, Italy

www: sites.unimi.it/camilloni

www: bioscienze.bio