**Requirements:**- PDB files

This command docks a structure of a protein/domain (probe) into a given cubic EM density map. See original paper for the description of the method and the most recommended protocols [Topfet al., 2005].

Note that this only works with cubic density maps.

The probe is specified by the variableem_pdb_name. Before starting the protocol, the probe is positioned on the EM density grid based on thestart_typevariable:

`'CENTER'`will translate the center of mass of the probe to the center of the grid.`'ENTIRE'`will divide the grid into cells similar in volume to the probe, and will translate the probe to the center of each of these cells consecutively.`'SPECIFIC'`will use the coordinates specified by the user (the input PDB coordinates) as a starting position.

The best fit between the probe and the EM density map is obtained by changing the position of the model so as to maximize the cross-correlation between the probe density and the EM density. SeeDensity.read()for the density fitting procedure, controlled by thedensity_typevariable.

The optimization of the cross-correlation score is performed by a 6D search of the probe on the EM grid, based on the variabletranslate_type. If'NONE'is specified, only a rotational search over the three rotational Euler angles (φ, θ, ψ) is performed, with no translations.angular_step_sizegives the maximal step size of searching for all combinations of Euler angles, which is recommended to be 30 degrees. The best fit from this coarse search is refined by a finer local search in all three Euler angles. For a protein of 150 residues this calculation typically takes less than 0.5 minutes on a 3.0 GHz Intel Xeon processor.

Iftranslate_typeis'RANDOM', a Monte Carlo (MC) optimization is performed, and the number of MC steps has to be specified (bynumber_of_steps). A single MC step consists of (i) a random translation of the probe for one voxel on the EM grid, (ii) a search for the three Euler angles that maximize cross-correlation score, and (iii) an application of the Metropolis criterion [Metropoliset al., 1953]. The temperature used for the Metropolis criterion is specified intemperature(typically about 5000 units). This calculation typically takes about 1-2 minutes.

Whentranslate_typeis'EXHAUSTIVE', a local search is performed with the probe on the grid. The optimal orientations at its original position and all 26 (i.e., 3x3x3 - 1) neighboring grid points are obtained successively by enumerating all three Euler angles. A Monte Carlo criterion is applied to each one of these 27 optimal orientations (usually with temperature lower than 5000, but this number has to be adjusted according to the optimization).number_of_stepsgives the number of steps for which this process is repeated (typically 25 times). When the EM density map covers only the probe model andstart_typeis either'CENTER'or'SPECIFIC', this protocol can be used for a translational and rotational refinement of the initial placement of the model on the grid. Whenstart_typeis'ENTIRE'this protocol will be applied for a local search only in those cells where the randomly oriented probe gives a positive cross-correlation score. The calculation typically takes about 10-15 minutes.

best_docked_modelsspecifies how many best-fitted models should be saved by the program. This becomes more important at decreasing resolutions, as the best solution will not necessarily have the highest cross-correlation score.

em_fit_output_filenames an output file which will be used to record the progress of the optimization.

**Output:****targ_1_1.pdb**- The fitted coordinates file. The name is formed by
taking the first 4 letters from your input PDB file and adding
`'_1_1.pdb'`. If*best_docked_models*= 2, you will get also targ_1_2.pdb, and so on. If you use the option*start_type*=`ENTIRE`, it will add targ_2_1.pdb, targ_2_2.pdb and so on. **bestCC_targ**- The results file which reports the CCF, with the number
of required solutions (as indicated in
*best_docked_models*). **targ_best.MRC**- The fitted structure converted to a map.
**targ_init_1.pdb**- The initial structure superposed in the center of
mass (if
*start_type*=`CENTER`), or in a specific location (if*start_type*=`SPECIFIC`). **targ_init.MRC**- The initial structure converted to a map.
**EM_map.MRC**- This is your original density map. It's a test to see if MODELLER is reading it correctly.

**Example: examples/commands/em_grid_search.py**-

from modeller import * log.verbose() env = Environ() den = Density(env, file='1cuk-a2.mrc', em_density_format='MRC', voxel_size=1., resolution=8., em_map_size=40, cc_func_type='CCF', density_type='SPHERE') den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=['1cuk-a2.pdb'], chains_num=[1], start_type='CENTER', number_of_steps=1, angular_step_size=30., temperature=0., best_docked_models=1, em_fit_output_file='test-cr.log')