Source code for cryosparc2.protocols.protocol_cryosparc_new_nonuniform_refine

# **************************************************************************
# *
# * Authors: Yunior C. Fonseca Reyna    (cfonseca@cnb.csic.es)
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# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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from pyworkflow import NEW
from pyworkflow.protocol.params import (FloatParam, Positive, IntParam,
                                        BooleanParam, EnumParam)
from .protocol_cryosparc_homogeneous_refine import ProtCryoSparc3DHomogeneousRefine


[docs]class ProtCryoSparcNewNonUniformRefine3D(ProtCryoSparc3DHomogeneousRefine): """ Apply non-uniform refinement to achieve higher resolution and map quality, especially for membrane proteins. Non-uniform refinement iteratively accounts for regions of a structure that have disordered or flexible density causing local loss of resolution. Accounting for these regions and dynamically estimating their locations can significantly improve resolution in other regions as well as overall map quality by impacting the alignment of particles and reducing the tendency for refinement algorithms to over-fit disordered regions. """ _label = '3D non-uniform refinement' _className = "nonuniform_refine_new" _devStatus = NEW def _defineParams(self, form): ProtCryoSparc3DHomogeneousRefine._defineParams(self, form) # ------------[Non-uniform Refinement]----------------- form.addSection(label='Advanced Refinement') form.addParam('refine_do_marg', BooleanParam, default=True, label="Adaptive Marginalization", help='Efficiently marginalize over poses and shifts ' 'using an auto-tuning adaptive sampling strategy. ' 'Can improve results on small molecules.') form.addParam('refine_nu_enable', BooleanParam, default=True, label="Non-uniform refine enable", help='Enable cross-validation-optimal non-uniform ' 'regularization during refinement.') form.addParam('refine_nu_filtertype', EnumParam, choices=['butterworth', 'rect', 'gaussian'], default=0, label="Non-uniform filter type", help='butterworth, rect, or gaussian') form.addParam('refine_nu_order', IntParam, default=8, validator=[Positive], label="Non-uniform filter order", help='Order of the butterworth filter used for ' 'cross-validation-optimal regularization. Default t' 'o 8, probably no need to change this.') form.addParam('refine_nu_awf', FloatParam, default=3, validator=[Positive], label="Non-uniform filter order", help='Adaptive Window Factor for cross-validation-optimal ' 'regularization. Trade off between fast transitions ' 'between regions (AWF should be lower) and more ' 'accurate local cross-validation test (AWF should ' 'be higher). Default of 3 is good, can try as low ' 'as 1.5 ') def _defineParamsName(self): """ Define a list with all protocol parameters names""" ProtCryoSparc3DHomogeneousRefine._defineParamsName(self) self._paramsName += ['refine_do_marg', 'refine_do_marg', 'refine_nu_filtertype', 'refine_nu_order', 'refine_nu_awf']