Re: [modeller_usage] grid_search and hetatm

[Modeller Caretaker <>]

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
--
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