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Re: [modeller_usage] grid_search and hetatm

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',

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
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