Examples

examples

Exanple script for generating and scoring torus maps in nuclear membrane fitting.

examples.examples.generate_bestfit_torus_map()

Fits several torus models onto the nuclear membrane and saves the best fit.

Returns:

None

Examples

fitter= bf.BagelFitter()

fitter.load_exprimental_map(os.path.join(data_path,"Yeast_C8_Double_MR_center.mrc" ))

tor_R_range=(660, 670, 10);
tor_r_range=(140, 160, 20);
tor_th_range=(55, 65, 10);
extension = 0.0

best_torus = fitter.fit_binary_torus(tor_R_range, tor_r_range, tor_th_range, extension)

fitter.write_torusmap_to_file(os.path.join(data_path,"torus_yeast_fitted.mrc" ))

examples.examples.generate_binary_torus_map()

Generates a binary torus map using predefined torus parameters and saves it to a file.

Returns:

None

Examples

data_path = os.path.join(script_dir,"./yeast_membrane/")

fitter= bf.BagelFitter()

tor_R = 660; tor_r=140; tor_th=55; extension=0.0

best_torus = fitter.generate_binary_torus(
        tor_R, tor_r, tor_th,
        extension=0.0,
        boundingbox_length=2240,
        voxel_size=10.0,
        outmap_fname=os.path.join(data_path,"torus_yeast_fitted.mrc" ))

examples.examples.score_torus_map_with_experimental_map()

Compares a generated torus map with an experimental map using a scoring function.

Returns:

None

Examples

fitter= bf.BagelFitter()

mapfile1 = os.path.join(data_path,"Yeast_C8_Double_MR_center.mrc" )

mapfile2 = os.path.join(data_path,"torus_yeast_fitted.mrc" )

fitter.score_torus_maps(mapfile1, mapfile2)