#======================================================================================= # # CTaskShelxeMR.py : CTaskShelxeMR(CCP4TaskWidget) # # Author : Kyle Stevenson,STFC # Created : 16th Sep. 2015, KJS # # Gui Class for refinement of MR solutions using Shelxe # #======================================================================================= from PyQt4 import QtGui,QtCore import CCP4TaskWidget import CCP4Widgets class CTaskAcorn(CCP4TaskWidget.CTaskWidget): TASKNAME = 'acorn' TASKVERSION = 1.0 TASKMODULE ='expt_phasing' TASKTITLE = "ACORN - Phase Refinement with Dynamic Density Modification" SHORTTASKTITLE = "ACORN" DESCRIPTION = "Un-biased improvement of initial phases for high resolution data (1.5 Angstoms and better)" ERROR_CODES = { 200 : { 'description' : 'Space group of reflection and phases file does not match' } } WHATNEXT = ['coot_rebuild','prosmart_refmac','buccaneer_build_refine_mr'] MGDISPLAYFILES = ['FPHIOUT'] def __init__(self, parent): CCP4TaskWidget.CTaskWidget.__init__(self,parent) def drawContents(self): self.setProgramHelpFile('acorn') # Comes in two varieties; version 1 needs the reflections & the model; version 2 also needs the phase info. folder1 = self.openFolder(folderFunction='inputData',title='Input Data') self.createLine( [ 'label', 'Run ACORN with ', 'widget', '-guiMode', 'radio', 'ACORN_PHSIN_TYPE' ] ) self.openSubFrame( frame=[True] ) self.createLine(['subtitle', 'Reflection Data','Integrated reflection data for experimental phasing.']) self.createLine( [ 'widget', 'F_SIGF' ] ) self.createLine( [ 'widget', 'ABCD' ], toggle=[ 'ACORN_PHSIN_TYPE', 'open', 'phases'] ) self.closeSubFrame() self.openSubFrame( frame=[True], toggle=[ 'ACORN_PHSIN_TYPE', 'open', 'model'] ) self.createLine(['subtitle', 'Model for approximate co-ordinates','Model for approximate co-ordinates (if known)']) self.createLine( ['widget', 'XYZIN'] ) self.closeSubFrame() self.createLine( [ 'tip', 'Extend the resolution of the data for use in ACORN', 'label', 'Artificially extend resolution','widget', 'ACORN_EXTEND', 'label',' to','widget', 'ACORN_EXTENDRES', 'label','Angstoms'] ) #self.openSubFrame( frame=[False], toggle=[ 'ACORN_EXTEND', 'open', [True] ] ) #self.createLine( [ 'tip', 'Resolution to extend to', 'label','Extend resolution to ','widget', 'ACORN_EXTENDRES', 'label','Angstoms' ] ) #self.closeSubFrame() self.createLine( [ 'tip', 'Apply resolution anisotropy correction to data', 'label', 'Anisotropy Correction','widget', 'ACORN_ANISOTROPY' ] ) folder2 = self.openFolder(folderFunction='acornGenParam',title='Advanced Acorn Parameters') self.createLine(['subtitle', 'General Run Parameters','General Parameter Choice']) self.createLine( [ 'tip', 'Custom ', 'widget', 'ACORN_BGRID', 'label', 'Choose a user defined grid size' ] ) self.openSubFrame( frame=[True], toggle=[ 'ACORN_BGRID', 'open', [True] ] ) self.createLine( [ 'tip', 'GRID keyword', 'label','Grid Size (Angstroms)','widget', 'ACOGEN_GRID' ] ) self.closeSubFrame() self.createLine( [ 'tip', 'Info', 'widget', 'ACORN_BSEED', 'label', 'Choose a user defined random number seed for ACORN' ] ) self.openSubFrame( frame=[True], toggle=[ 'ACORN_BSEED', 'open', [True] ] ) self.createLine( [ 'tip', 'SEED keyword', 'label','Random Number Seed','widget', 'ACOGEN_SEED' ] ) self.closeSubFrame() #folder3 = self.openFolder(folderFunction='acornReflectParam',title='Selection of Reflection Data') self.createLine(['subtitle', 'Selection of Reflection Data','Reflection Data Settings']) self.createLine( [ 'tip', 'Use reflections within resolution range if ticked, all data used otherwise', 'widget', 'ACORN_BRESOL', 'label', 'User defined resolution range for reflection data' ] ) self.openSubFrame( frame=[True], toggle=[ 'ACORN_BRESOL', 'open', [True] ] ) self.createLine( [ 'tip', 'RESOLUTION keyword, Low Resolution Limit', 'label','Use reflections within resolution limit of ', 'widget', 'ACOREF_RESOLL', 'label', 'Angstrom' ] ) self.createLine( [ 'tip', 'RESOLUTION keyword, High Resolution Limit', 'label','to a limit of', 'widget', 'ACOREF_RESOLU', 'label', 'Angstrom' ] ) self.closeSubFrame() self.createLine( [ 'tip', 'The reflections with FP less than cut*SIGFP will be rejected and treated as extended reflections', 'widget', 'ACORN_BEXCLUDE', 'label', 'Exclude low SIGFP reflections' ] ) self.openSubFrame( frame=[True], toggle=[ 'ACORN_BEXCLUDE', 'open', [True] ] ) self.createLine( [ 'tip', 'EXCLUDE keyword', 'label','Reject reflections that are less than ','widget', 'ACOREF_EXCLUDE' ,'label', '* the standard deviation (sigma)' ] ) self.closeSubFrame() self.createLine( [ 'tip', 'The reflections with E-values greater than a certain cut will be rejected', 'widget', 'ACORN_BECUT', 'label', 'Exclude reflections that are high E-value outliers' ] ) self.openSubFrame( frame=[True], toggle=[ 'ACORN_BECUT', 'open', [True] ] ) self.createLine( [ 'tip', 'ECUT keyword', 'label','Reject observed reflections with E-values greater than ','widget', 'ACOREF_ECUT' ] ) self.closeSubFrame() #folder4 = self.openFolder(folderFunction='acornPhasePar',title='Acorn Phase Parameters') self.createLine(['subtitle', 'Acorn Phase Settings','Phase Settings']) self.createLine( [ 'tip', 'SUPP keyword', 'widget', 'ACOPH_PATSUP', 'label','Use the Paterson Superposition Function' ] ) self.createLine( [ 'tip', 'NTRY keyword', 'label','Number of Trials','widget', 'ACOPH_NUMTRIALS' ] ) self.createLine( [ 'tip', 'MAXSET keyword', 'label', 'Number of initials phase sets to refine','widget', 'ACOPH_MAXSET' ] ) self.createLine( [ 'tip', 'CUTDDM keyword', 'label', 'Upper density limit for Dynamic Density Modification (DDM)','widget', 'ACOPH_CUTDDM' ] ) self.createLine( [ 'tip', 'PSFINISH keyword', 'label', 'Cease DDM cycling if phase shift between consecutive cycles is less than','widget', 'ACOPH_PSFINISH' ] ) self.createLine( [ 'tip', 'CCFINISH keyword', 'label', 'Cease phase refinement if correlation coefficient exceeds','widget', 'ACOPH_CCFINISH' ] ) self.openSubFrame( frame=[True], toggle=[ 'ACORN_PHSIN_TYPE', 'open', 'model'] ) self.createLine(['subtitle', 'Model Input Settings','Model Settings']) self.createLine( [ 'label', 'Run ACORN with ', 'widget', '-guiMode', 'radio', 'ACORN_MODEL_USE' ] ) # Several options available . Use ACORN_MODEL_SELECT, 3 options. # Use All Atoms (already the default) # Use Single Fragment of a certain length starting at a particular atom. NAFRAG from NSTART # Use Number of fragments, of fixed length. POSI number of fragments, at length NAFRAG. self.createLine( [ 'tip', 'The start position of the fragment in the model file', 'label','Start fragment at atom number ','widget', 'ACORN_NSTART' ], toggle=[ 'ACORN_MODEL_USE', 'open', 'one']) self.createLine( [ 'tip', 'Fragment is this long in terms of atoms', 'label','Length of fragment ','widget', 'ACORN_NAFRAG' ], toggle=[ 'ACORN_MODEL_USE', 'open', 'one']) self.createLine( [ 'tip', 'Number of fragments in set', 'label','Number of fragments to pick ','widget', 'ACORN_POSI' ], toggle=[ 'ACORN_MODEL_USE', 'open', 'set']) self.createLine( [ 'tip', 'Length of each fragment', 'label','Length of each fragment ','widget', 'ACORN_NAFRAG' ], toggle=[ 'ACORN_MODEL_USE', 'open', 'set']) self.closeSubFrame() def taskValidity(self): import CCP4ErrorHandling rv = CCP4ErrorHandling.CErrorReport() # Check the space group is same in both input Mini-MTZ files if self.container.inputData.F_SIGF.exists(): fsig_sg = str(self.container.inputData.F_SIGF.fileContent.spaceGroup) else: fsig_sg = None if self.container.inputData.ABCD.exists(): phifom_sg = str(self.container.inputData.ABCD.fileContent.spaceGroup) else: phifom_sg = None if fsig_sg is not None and phifom_sg is not None and fsig_sg != phifom_sg: rv.append(self.__class__,200,details='Reflections file space group:'+ fsig_sg +' Phases file space group:'+ phifom_sg ,stack=False) return rv