phenix.protocols.protocol_search_fit module

class phenix.protocols.protocol_search_fit.PhenixProtSearchFit(**kwargs)[source]

Bases: phenix.protocols.protocol_refinement_base.PhenixProtRunRefinementBase

given a chain of n alanines, a 3D map and a sequence search for the subsequence of n aminoacids that better fits in the density. Only works if the atomic structure has a single chain

FITTEDFILE = 'fitted.mrc'
createOutputStep()[source]
createTable()[source]

Create table and clean it if needed

extractNumber(filename)[source]
mutateStep(firstaa, firstAAinChain, atomStructSize, chainName, numberOfSteps)[source]

mutate atom struct inputStructure using aa in sequence inputSequence starting at firstaa

refineStep2()[source]