6. Density Map Generation

class StructureBlurrer.StructureBlurrer

A class to generates a density map from a structure instance.

gaussian_blur(prot, resolution, densMap=False, sigma_coeff=0.356, normalise=True, filename='None')

Returns a Map instance based on a Gaussian blurring of a protein.

Arguments:

prot

the Structure instance to be blurred.

resolution

the resolution, in Angstroms, to blur the protein to.

densMap

False to build a Map with dimensions based on the protein, or a Map instance to be used as a template.

sigma_coeff

the sigma value (multiplied by the resolution) that controls the width of the Gaussian. Default values is 0.356.

Other values used :

0.187R corresponding with the Gaussian width of the Fourier transform falling to half the maximum at 1/resolution, as used in Situs (Wriggers et al, 1999);

0.356R corresponding to the Gaussian width at 1/e maximum height equaling the resolution, the default in Chimera (Petterson et al, 2004);

0.425R the fullwidth half maximum being equal to the resolution, as used by FlexEM (Topf et al, 2008);

0.5R the distance between the two inflection points being the same length as the resolution, an option in Chimera (Petterson et al, 2004);

1R where the sigma value simply equal to the resolution, as used by NMFF (Tama et al, 2004).

filename

output name of the map file.

gaussian_blur_box(prot, resolution, box_size_x, box_size_y, box_size_z, densMap=False, sigma_coeff=0.356, normalise=True, filename='None')

Returns a Map instance based on a Gaussian blurring of a protein.

Arguments:

prot

the Structure instance to be blurred.

resolution

the resolution, in Angstroms, to blur the protein to.

box_size_x

x dimension of map box in Angstroms.

box_size_y

y dimension of map box in Angstroms.

box_size_z

z dimension of map box in Angstroms.

densMap

False to build a Map with dimensions based on the protein, or a Map instance to be used as a template.

sigma_coeff

the sigma value (multiplied by the resolution) that controls the width of the Gaussian. Default values is 0.356.

Other values used :

0.187R corresponding with the Gaussian width of the Fourier transform falling to half the maximum at 1/resolution, as used in Situs (Wriggers et al, 1999);

0.356R corresponding to the Gaussian width at 1/e maximum height equaling the resolution, the default in Chimera (Petterson et al, 2004);

0.425R the fullwidth half maximum being equal to the resolution, as used by FlexEM (Topf et al, 2008);

0.5R the distance between the two inflection points being the same length as the resolution, an option in Chimera (Petterson et al, 2004);

1R where the sigma value simply equal to the resolution, as used by NMFF (Tama et al, 2004).

filename

output name of the map file.

make_atom_overlay_map(densMap, prot)

Returns a Map instance with atom masses superposed on it.

Arguments:

densMap

an empty (all densities zero) Map instance to superpose the atoms onto.

prot

a Structure instance.

make_atom_overlay_map1(densMap, prot)

Returns a Map instance with atom locations recorded on the nearest voxel with a value of 1.

Arguments:

densMap

an empty (all densities zero) Map instance to superpose the atoms onto.

prot

a Structure instance.

mapGridPosition(densMap, atom)

Returns the index of the nearest pixel to an atom, and atom mass (4 values in list form).

Arguments:

densMap

Map instance the atom is to be placed on.

atom

Atom instance.

protMap(struct, apix, resolution, filename='None')

Returns an Map instance sized and centred based on the atomic structure.

Arguments:

apix

Angstroms per pixel for the Map to be outputted.

resolution

Target resolution of the outputted map.

sigma_coeff

Sigma width of the Gaussian used to blur the atomic structure.

filename

output name of the map file.