continuousflex.protocols.protocol_nma_alignment_vol module

class continuousflex.protocols.protocol_nma_alignment_vol.FlexProtAlignmentNMAVol(**kwargs)

Bases: pwem.protocols.protocol_3d.ProtAnalysis3D

Protocol for rigid-body and elastic alignment for volumes using NMA. This protocol is the code module of HEMNMA-3D. It will take as input a set of normal modes calculated for an input atomic or pseudoatomic structure, and a set of volumes (subtomograms) to analyze. It fits the input structure using its modes (a subset of the modes need to be selected) into each one of the input volumes while simultaneously looking for rigid-body alignment, with compensation for missing wedge artefacts. The result of this protocol are rigid-body and elastic parameters for each input volume. Those results will be fed for a dimensionality reduction method (nma dimred vol) for further processing.

convertInputStep(atomsFn)

copyDeformationsStep(deformationMd)

createOutputStep()

getInputPdb()

Return the Pdb object associated with the normal modes.

performNmaStep(atomsFn, modesFn)

writeModesMetaData()

Iterate over the input SetOfNormalModes and write the proper Xmipp metadata. Take into account a possible selection of modes