Source code for relion.protocols.protocol_localres

# **************************************************************************
# *
# * Authors:     Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk) [1]
# *              J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [2]
# *
# * [1] MRC Laboratory of Molecular Biology, MRC-LMB
# * [2] SciLifeLab, Stockholm University
# *
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# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
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# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * GNU General Public License for more details.
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# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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from pwem.emlib.image import ImageHandler
import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params

import relion
import relion.convert
from .protocol_postprocess import ProtRelionPostprocess


[docs]class ProtRelionLocalRes(ProtRelionPostprocess): """ This protocol does local resolution estimation using Relion. This program basically performs a series of post-processing operations with a small soft, spherical mask that is moved over the entire map, while using phase-randomisation to estimate the convolution effects of that mask. """ _label = 'local resolution' def _createFilenameTemplates(self): """ Centralize how files are called for iterations and references. """ myDict = { 'half1': self._getInputPath("relion_half1_class001_unfil.mrc"), 'half2': self._getInputPath("relion_half2_class001_unfil.mrc"), 'outputVolume': self._getExtraPath('relion_locres_filtered.mrc'), 'resolMap': self._getExtraPath('relion_locres.mrc'), 'solventMask': self._getExtraPath('input_solvent_mask.mrc') } self._updateFilenamesDict(myDict) # -------------------------- DEFINE param functions ----------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('protRefine', params.PointerParam, pointerClass="ProtRefine3D", label='Select a previous refinement protocol', help='Select any previous refinement protocol to get the ' '3D half maps. Note that it is recommended that the ' 'refinement protocol uses a gold-standard method.') form.addParam('solventMask', params.PointerParam, pointerClass='VolumeMask', allowsNull=True, label='User-provided solvent mask', help='Provide a mask with values between 0 and 1 ' 'around all domains of the complex. ResMap uses ' 'this mask for local resolution calculation. ' 'RELION does NOT use this mask for calculation, ' 'but makes a histogram of local resolution ' 'within this mask.') form.addParam('calibratedPixelSize', params.FloatParam, default=0., label='Calibrated pixel size (A)', help="Provide the final, calibrated pixel size in " "Angstroms. If 0, the input pixel size will be used. " "This value may be different from the pixel-size " "used thus far, e.g. when you have recalibrated " "the pixel size using the fit to a PDB model. " "The X-axis of the output FSC plot will use this " "calibrated value.") form.addParam('bfactor', params.FloatParam, default=-100., label='Provide B-factor:', help='Probably, the overall B-factor as was ' 'estimated in the postprocess is a useful ' 'value for here. Use negative values for ' 'sharpening. Be careful: if you over-sharpen ' 'your map, you may end up interpreting ' 'noise for signal!') group = form.addGroup('MTF') group.addParam('mtf', params.FileParam, label='MTF of the detector', help='User-provided STAR-file with the MTF-curve ' 'of the detector.' 'Relion param: <--mtf>') group.addParam('origPixelSize', params.FloatParam, default=-1.0, label='Original detector pixel size (A)', help='This is the original pixel size (in Angstroms)' ' in the raw (non-super-resolution!) micrographs') form.addSection(label='LocalRes') form.addParam('Msg', params.LabelParam, label='Select Advanced level if you want to adjust the ' 'parameters') form.addParam('locResSamp', params.IntParam, default=25, label='Sampling rate (A)', expertLevel=params.LEVEL_ADVANCED, help='Sampling rate (in Angstroms) with which to ' 'sample the local-resolution map') form.addParam('locResMaskRad', params.IntParam, default=-1, label='Mask radius (A)', expertLevel=params.LEVEL_ADVANCED, help='Radius (in A) of spherical mask for ' 'local-resolution map (default = 0.5*sampling)') form.addParam('locResEdgeWidth', params.IntParam, default=-1, label='Edge width (A)', expertLevel=params.LEVEL_ADVANCED, help='Width of soft edge (in A) on masks for ' 'local-resolution map (default = sampling)') form.addParam('locResRand', params.FloatParam, default=25.0, label='Randomize phases from (A)', expertLevel=params.LEVEL_ADVANCED, help='Randomize phases from this resolution (in A)') form.addParam('locResMin', params.IntParam, default=50, label='Lowest res limit (A)', expertLevel=params.LEVEL_ADVANCED, help='Lowest local resolution allowed (in A)') form.addParallelSection(threads=0, mpi=1) # -------------------------- INSERT steps functions ----------------------- # ------------------------- STEPS functions -------------------------------
[docs] def convertInputStep(self, protId): pwutils.makePath(self._getInputPath()) protRef = self.protRefine.get() vol = protRef.outputVolume newDim = vol.getXDim() newPix = vol.getSamplingRate() half1, half2 = vol.getHalfMaps().split(',') ih = ImageHandler() ih.convert(half1, self._getFileName("half1")) ih.convert(half2, self._getFileName("half2")) if self.solventMask.hasValue(): relion.convert.convertMask(self.solventMask.get(), self._getFileName('solventMask'), newPix, newDim)
# -------------------------- INFO functions ------------------------------- def _summary(self): summary = [] if not hasattr(self, 'outputVolume'): summary.append("Output volume not ready yet.") else: output = self.outputVolume summary.append("%s: Output volume was locally filtered " "and sharpened" % self.getObjectTag(output)) return summary # -------------------------- UTILS functions ------------------------------ def _defineParamDict(self): """ Define all parameters to run relion_postprocess""" volume = self.protRefine.get().outputVolume # It seems that in Relion3 now the input should be the map # filename and not the prefix as before inputFn = self._getFileName('half1') cps = self.calibratedPixelSize.get() angpix = cps if cps > 0 else volume.getSamplingRate() self.paramDict = {'--i': inputFn, '--o': self._getExtraPath('relion'), '--angpix': angpix, '--adhoc_bfac': self.bfactor.get(), '--locres': '', # Expert options '--locres_sampling': self.locResSamp.get(), '--locres_maskrad': self.locResMaskRad.get(), '--locres_edgwidth': self.locResEdgeWidth.get(), '--locres_randomize_at': self.locResRand.get(), '--locres_minres': self.locResMin.get() } mtfFile = self.mtf.get() if mtfFile: self.paramDict['--mtf'] = mtfFile if self.origPixelSize.get() != -1.0: self.paramDict['--mtf_angpix'] = self.origPixelSize.get() if self.solventMask.hasValue(): self.paramDict['--mask'] = self._getFileName('solventMask') def _getRelionMapFn(self, fn): return fn.split(':')[0] def _getMaskFn(self): return self._getPath('solvent_mask.mrc')