Consensus Scoring of multiple fits in a cryoEM map

class Consensus.Consensus[source]

A class to clustering an ensemble of structure instance

vote(ensemble_list, score_list, res_target_map, sigma_coeff, number_top_mod=0, write=False, targetMap=False)[source]

Borda consensus scoring calculation between multiple “fits” using a user defined set of scores. The Borda count is a single-winner election method in which voters rank candidates in order of preference.

Arguments:
ensemble_list
Input list of Structure Instances.
score_list

Input list of scoring function to use.

See ScoringFunctions class for a list of the available Scoring Function. E.g. set score=’CCC’ to use the Cross-correlation coefficient.

Score option are:

i ‘CCC’ - Cross-correlation coefficient;

ii ‘LAP’ - Laplacian-filtered cross-correlation coefficient: useful for maps with resolutions worse than 10-15 A;

iii ‘MI’ - Mutual information score: a good and robust score but relatively slow to calculate;

iv ‘ENV’ - Envelope score: the fastest score to calculate due to binarisation of the map.

v-vii ‘NV’,’NV_Sobel’,’NV_Laplace’- Normal vector score: a vector-based surface superimposition score with or without Sobel/Laplace filter.

viii ‘CD’ - Chamfer Distance: a score used in computer vision algorithms as a fast similarity metric

res_target_map
the resolution, in Angstroms, of the target Map.
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);

0.225R which makes the Fourier transform of the distribution fall to 1/e of its maximum value at wavenumber 1/resolution, the default in Chimera (Petterson et al, 2004)

0.356R corresponding to the Gaussian width at 1/e maximum height equaling the resolution, an option 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).

number_top_mod
Number of Fits to cluster. Default is all.
write
True will write out a file that contains the list of the structure instances representing different fits scored and clustered. note the lrms column is the Calpha RMSD of each fit from the first fit in its class
targetMap
Target Map Instance.
vote_list(score_lists)[source]

Borda consensus scoring calculation between multiple “fits” using a user defined set of scores. The Borda count is a single-winner election method in which voters rank candidates in order of preference.

Arguments:
ensemble_list
Input list of Structure Instances.
score_list
Input list of list. Each list is a list of Structure Instances associated with a score.
vote_mode(ensemble_list, score_list, res_target_map, sigma_coeff, number_top_mod=0, write=False, targetMap=False)[source]

Mode consensus scoring calculation between multiple “fits” using a user defined set of scores.

Arguments:
ensemble_list
Input list of Structure Instances.
score_list

Input list of scoring function to use.

See ScoringFunctions class for a list of the available Scoring Function. E.g. set score=’CCC’ to use the Cross-correlation coefficient.

Score option are:

i ‘CCC’ - Cross-correlation coefficient;

ii ‘LAP’ - Laplacian-filtered cross-correlation coefficient: useful for maps with resolutions worse than 10-15 A;

iii ‘MI’ - Mutual information score: a good and robust score but relatively slow to calculate;

iv ‘ENV’ - Envelope score: the fastest score to calculate due to binarisation of the map.

v-vii ‘NV’,’NV_Sobel’,’NV_Laplace’- Normal vector score: a vector-based surface superimposition score with or without Sobel/Laplace filter.

viii ‘CD’ - Chamfer Distance: a score used in computer vision algorithms as a fast similarity metric

res_target_map
the resolution, in Angstroms, of the target Map.
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);

0.225R which makes the Fourier transform of the distribution fall to 1/e of its maximum value at wavenumber 1/resolution, the default in Chimera (Petterson et al, 2004)

0.356R corresponding to the Gaussian width at 1/e maximum height equaling the resolution, an option 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).

number_top_mod
Number of Fits to cluster. Default is all.
write
True will write out a file that contains the list of the structure instances representing different fits scored and clustered. note the lrms column is the Calpha RMSD of each fit from the first fit in its class
targetMap
Target Map Instance.