On 12/21/17 1:36 AM, Carlo Camilloni wrote: > 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?

Looking at the code, it should be supported (although I don't think it's ever been tested - it's debatable whether the fit of the cofactors into the density is handled correctly). But you've asked the algorithm to read a single chain from 'struct' (chains_num=[1]). I don't see your PDB file, but maybe the cofactors are in a different chain?

Ben Webb, Modeller Caretaker