SedAnal 10 file format, written by SedAnal v7.67 on 2022-05-24 16:23:56 (SedAnal.exe is in C:\SEDANAL\Program 7.67) owner "" last name of person responsible for this copy of SedAnal nPreferenceUsers 1 # of users 748 preferenceUserCurrent 0 Current user # 748 preferencesameDir TRUE Use same dir for preference file as SedAnal.exe 755 userName "???" current user name 748 preferenceFilePath "C:\SEDANAL\Program 7.67\Preferences.txt" full path to this preference file 748 key 432 for developer use; 0 for other users databaseKey 77777777 unique identifier for your experiment database dataDir "AUCMWLDATA" top-level user data directory modelDir "ModelEditor" directory containing the model information file used by SedAnal recentControlFilesMax 99 number of recent control filenames to retain between sessions imageFormat 2 saved screen images are 0=PNG 1=JPEG 2=bmp plotInitMax 30 max # scans to plot in preprocessor preprocessorInstructions FALSE display instructions preprocessor stepsInPreprocessor FALSE force preprocessor parameters to be done in order showAttentionBoxes FALSE show indicator for next parameter to be chosen in preprocessor exptTreeDisable FALSE disable the experiment tree in preprocessor and dc/dt (user must browse) experimentInfoOldFiles FALSE ask to add exp info in existing run files experimentInfoNewFiles FALSE ask to add exp info in new run files sameWavelengthTolerance 4 maximum scan wavelengths can differ to be considered same speedTolerance 0 maximum RPM speeds can differ to be considered same 764 showAxisX TRUE show x-axis on preprocessor plot 594 showAxisY FALSE show y-axis on preprocessor plot 594 showNumberOfScans TRUE show # scans/total scans on preprocessor plot 594 showScaleX 2 0=none, 1=ticks, 2=grid for preprocessor plot 594 showScaleY 2 0=none, 1=ticks, 2=grid for preprocessor plot 594 preprocPlotPointSize 100 preprocessor plot point size (0=1 pixel, else diameter of solid circle) scanSelectChoice 1 0=checkboxes always, 1=grid always, 2=checkboxes <1000 scans, else grid 751 apprEqDScan0 9801 difference between final scan sequence and initial scan to be compared 754 apprEqDScan1 0 diff between final scan sequence and scan to be used as reference; usu 0 754 apprEqDr0 0.01 difference from meniscus to initial radius to be used for comparison 754 apprEqDr1 0.002 difference between final radius and cell base to be used for comparison 754 apprEqDr 0.0005 spacing of uniform grid onto which experimental scans are interpolated 754 apprEqPlotColor 255 color of the RMSD plot symbols 754 apprEqPlotType 6 size & shape of the RMSD plot symbols 754 apprEqPlotConnect FALSE RMSD plot symbols are to be connected 754 apprEqPlotColor2 32768 color of the angle plot symbols 766 apprEqPlotType2 6 size & shape of the angle plot symbols 766 apprEqPlotConnect2 FALSE angle plot symbols are to be connected 766 apprEqPlotWhich 2 which app to eq plot(s) are shown (0=none, 1=RMSD 2=angle 3=both 766 showScanSummary TRUE show the scan summary window 766 BioSpinButtons12 110010 which plots appear in plot windows 1 and 2 BioSpinButtons3 1110 which plots appear in plot window 3 BioSpinErrorBars TRUE show error bars BioSpinLog TRUE plot log of input data in plot window 4 BioSpinMin 0 minimum for 2-species plots in plot window 3 BioSpinMax 9 maximum BioSpinFitDegree 2 fit data to polynomial of this degree BioSpinNPoints 10 minimum points for least-squares fitting BioSpinRange 0.5 minimum concentration range for least-squares fitting nDcdtSGridPoints 500 number of s* grid points nDcdtRGridPoints 1000 number of radial grid points for input data nPlateauIterations 1 number of iterations used for WDA plateau processing dcdtPlotShow 3 what to show in dc/dt vs s* plot WDAPlotShow 2 what to show in WDA plot gPlotShow 1 what to show in gHat vs s* plot dcdtDoWide TRUE default is WDA dcdtComputeWtAvg FALSE compute weight averages dcdtDoInterpolation TRUE do interpolation dcdtUseUnsmoothed TRUE use unsmoothed to calc S.E.M. for WDA 726 dcdtLogPlot FALSE default is log plot dcdtLogBase10 TRUE logs are base 10 dcdtLogScaleX TRUE x-axis log-scaled dcdtLogScaleY FALSE y-axis log-scaled dcdtSmoothingPercent 1 smoothing percent dcdtSSpacing 0.01 s* grid spacing dcdtReportColSeparator [none] char which separates columns in dc/dtreport files WDARadius0 6.1 WDA radius grid r0 651 WDARadius1 7.2 WDA radius grid r1 651 WDARadiusInc 0.01 WDA radius grid increment 651 WDARadiiCalc(1) "bbbbbbbbbbbbbbb$###" default radial points to calculate 651 WDARadiiCalc(2) "" default radial points to calculate 651 WDARadiiCalc(3) "" default radial points to calculate 651 WDARadiiPlot(1) "#####bbb*##########" default radial points to plot 651 WDARadiiPlot(2) "" default radial points to plot 651 WDARadiiPlot(3) "" default radial points to plot 651 dcdtAvgLineWidth 2 width of the line of averages in plots dumpDcdtData 0 non-0 to write debugging info to DcdtData.txt dcdtReportDir "C:\SEDANAL\LIBRARY" directory where links to reports are stored dcdtCopyReports FALSE make a copy of dc/dt reports instead of link rFractDcdt0 0.153846 fract of r omit dc/dt auto-scale, men rFractDcdt1 0.230769 fract of r omit dc/dt auto-scale, base rFractWDA0 0.153846 fract of r omit WDA auto-scale, men rFractWDA1 0.230769 fract of r omit WDA auto-scale, base plotErrorBars(1) FALSE show error bars for dc/dt ,g/gHat, WDA plot plotErrorBars(2) FALSE show error bars for dc/dt ,g/gHat, WDA plot plotErrorBars(3) FALSE show error bars for dc/dt ,g/gHat, WDA plot plotErrorBarColor(1) 8421504 color of error bars for dc/dt ,g/gHat, WDA plot plotErrorBarColor(2) 8421504 color of error bars for dc/dt ,g/gHat, WDA plot plotErrorBarColor(3) 255 color of error bars for dc/dt ,g/gHat, WDA plot maxNMers 123 maximum number of n-mers to be computed for infinite self-association polyMeth ISOENR polymerization method expCoeffsS 0 2/3 0 0 a0, a1, a2 a3 in dependence of s on n-mer maxIterations 100000 maximum number iterations for fitting concUnitsControl g/L default units for loading concentrations loadConcInputType 3 how load conc for comp>1 are input 499 controlScreenNSigDig 9 # sig fig for reals on control screen 499 controlScreenSizeX 1 relative size of control screen, horizontal (x) 499 controlScreenSizeY 1 relative size of control screen, vertical (y) 499 stdDevAbsorbanceScans 0.005 default std dev for absorbance data 692 stdDevInterferenceScans 0.005 default std dev for interference data 692 stdDevIntensityScans 54.7723 default std dev for intensity data 692 stdDevFluorescenceScans 45.2548 default std dev for fluorescence data 692 stdDevOtherScans 1 default std dev for other data 692 weightingChoice 0 0=no weighting 1=by cell type 2=plateau 3=use point std dev perturbMin 0 minimum number of times to perturb and refit after best fit perturbMax 0 maximum number of times to perturb and refit after best fit perturbFractChg 0.01 minimum fractional change in fit criterion to continue perturbing perturbAll FALSE use perturbations on every bootstrap/Monte Carlo fit maxRunsToPlot 12 maximum number of plots on the fitting screen at once maximizeFitWindow FALSE expand the fitting window to fit the screen paramFmt "%11.4E" during fitting, C++ format used to display params 745 gridTypeX GRID marking for fitting plots, x-axis 517 gridTypeY GRID marking for fitting plots, y-axis 517 labelPlots TRUE label the plots showCellNumPlots TRUE number the plots showCellStatPlots TRUE dispaly fit statistic in the plots fitMethod 2 1=use simplex 2=use Levenberg-Marquardt obsColor 255 color in fitting screen for observed data calc0Color 65280 color in fitting screen for first calculated delta-c calc1Color 65280 color in fitting screen for last calculated delta-c resColor 16711680 color in fitting screen for residuals eqCalcColor 16711680 color in fitting screen for equilibrium calculator axisColor 12632256 color in fitting screen for axes ticksColor 0 color in fitting screen for ticks descrColor 0 font color in fitting screen for description 757 descrBkgndColor 65535 background color in fitting screen for description 757 cellNumColor 0 font color in fitting screen for cell # 757 cellNumBkgndColor 12648384 background color in fitting screen for cell # 757 fitStatColor 0 font color in fitting screen for fit stat 757 fitStatBkgndColor 10535167 background color in fitting screen for fit stat 757 descrPos 0 where to position description in plots 757 cellNumPos 1 where to position cell # in plots 757 fitStatPos 1 where to position fit stat in plots 757 optColor 12632256 color in menu which outlines options fitExpScreenPointSize 7 size of data points on fitting screen fitExpPrintPointSize 1 size of data points on printed output fitResidScreenPointSize 6 size of residuals on fitting screen fitResidPrintPointSize 1 size of residuals on printed output calc0Width 3 line thickness in fitting screen for first calculated delta-c calc1Width 3 line thickness in fitting screen for last calculated delta-c simulationWritesAbr TRUE Simulating data writes a run file simulationWritesScans TRUE Simulating data writes scan files simulationWritesControl TRUE Simulating data writes a prototype control file controlFileCopy TRUE Fitting data makes a numbered copy of the control file sRatioDefaultLimit [none] default limit for s/so DRatioDefaultLimit [none] default limit for D/Do minimize 1 statistic to be minimized during fitting relStdDevToExit 1e-09 relative change in fitting criterion to stop sed vel fit relStdDevToExitEq 1e-12 relative change in fitting criterion to stop equil fit simplexInitMethod 3 which of several methods is used to initialize the simplex LMScale TRUE scale parameters in L-M sed vel fit LMScaleEq TRUE scale parameters in L-M eq fit relParToExit 1e-15 relative change in parameters to stop L-M sed vel fit relParToExitEq 1e-15 relative change in parameters to stop L-M eq fit relErrorInFunc 0 relative change in function for numerical derivatives for L-M sed vel fit relErrorInFuncEq 0 relative change in function for numerical derivatives for L-M eq fit relStdSSQ 1e-15 relative change in sum of squares to stop L-M sed vel fit relStdSSQEq 1e-15 relative change in sum of squares to stop L-M eq fit orthogToExit 1e-15 orthogonality between parameters and derivatives to stop L-M sed vel fit orthogToExitEq 1e-15 orthogonality between parameters and derivatives to stop L-M eq fit LMStepBound 100 relative initial step bound in L-M sed vel fit LMStepBoundEq 100 relative step size for numerical derivatives L-M eq fit maxKIntSteps 10000 maximum steps in the kinetic integrator kIntAccuracy 1e-06 minKIntStep 1e-10 minimum step size in the kinetic integrator krEquilibrium 0.01 reverse rate constant to be used if Keq given initialEquilKinMeth 2 3 3 method for kinetics/equilibrium 458 runEquilKinMeth 2 3 1 method for kinetics/equilibrium 458 equilibFitEquilKinMeth 2 3 1 method for kinetics/equilibrium equilMaxChg 1e-13 largest fractional concentration change allowed at equilibrium stepChgLimit 0.01 fractional concentration change limit for conc(t) stepSizeHalved 6 how many of times equilibrating time step may be halved numSteps 6 times kinetic integrator step limit can be doubled during equilibration NRfChgMin 1e-10 fractional function magnitude change limit for N-R successive approx NRChgMin 1e-08 fractional component concentration change limit for N-R successive approx clavDtInitial 0.01 clavConcChange 0.02 clavConcFracLimit 1e-06 clavDtChange0 1.02 clavDtChange1 1.02 nTimeStepTries 4 times Claverie can reduce the time step to overcome invalid concentrations nPointsDefFitSE 500 default # points for sed eq fits nPointsDefFitSV 500 default # points for sed vel fits nPointsDefSimSE 1500 default # points for sed eq simulations nPointsDefSimSV 1500 default # points for sed vel simulationss negativeContinue TRUE whether Claverie should continue if it encounters negative concentrations nSpacings 1 number of grid spacings for Claverie simulation fractDist(1) 1 Fraction meniscus-base for density 1 fractDist(2) [none] Fraction meniscus-base for density 2 fractDist(3) [none] Fraction meniscus-base for density 3 gridDens(1) 1 Relative density in region 1 gridDens(2) [none] Relative density in region 2 gridDens(3) [none] Relative density in region 3 nSubsets 0 the number of subsets of the data to be refitted errEstMethod 0 choice of error estimation in fitted parameters FStatistics FALSE whether F-statistics should be used to estimate errors FFormula 0 choice of formula for target F in F-statistics confidenceLevel 0.95 confidence level for F-statistics FStatErrInConf 0.01 tolerance in fractional part of confidence level for F-statistics FS_maxAddlFits 16 max tries for fit in F-statistics FIncM 0.005 FALSE initial fractional increment in F-statistics for parameter type M FIncS 0.005 FALSE initial fractional increment in F-statistics for parameter type s FIncD 0.01 FALSE initial fractional increment in F-statistics for parameter type D FIncDensIncr 0.01 FALSE initial fractional increment in F-statistics for parameter type densIncr FIncExtCoeff 0.01 FALSE initial fractional increment in F-statistics for parameter type ext coeff FIncK 0.1 FALSE initial fractional increment in F-statistics for parameter type kf/kr/K FIncLoadConc 0.01 FALSE initial fractional increment in F-statistics for parameter type load conc FIncMb 0.01 TRUE initial absolute increment in F-statistics for parameter type men,base FIncYOff 0.005 TRUE initial absolute increment in F-statistics for parameter type yOff FIncF 0.005 TRUE initial absolute increment in F-statistics for parameter type f/fo FIncKs 0.01 FALSE initial fractional increment in F-statistics for parameter type Ks FIncKs2 0.01 FALSE initial fractional increment in F-statistics for parameter type Ks2 FIncBM1 0.01 FALSE initial fractional increment in F-statistics for parameter type BM1 FIncCM1 0.01 FALSE initial fractional increment in F-statistics for parameter type CM1 FIncTheta 0.01 FALSE initial fractional increment in F-statistics for parameter type theta FIncTemp 0.01 FALSE initial fractional increment in F-statistics for parameter type temp FIncDens 0.01 FALSE initial fractional increment in F-statistics for parameter type dens FIncViscR 0.01 FALSE initial fractional increment in F-statistics for parameter type viscR FIncUserAux1 0.01 FALSE initial fractional increment in F-statistics for parameter type user aux FIncUserAux2 0.01 FALSE initial fractional increment in F-statistics for parameter type user aux ComprChoiceDcdt 0 default compressibility choice for SV 682 ComprValueDcdt 4.591e-11 default compressibility fixed value for SV 682 ComprChoiceWDA 0 default compressibility choice for SV 682 ComprValueWDA 4.591e-11 default compressibility fixed value for SV 682 ComprChoiceSE 0 default compressibility choice for SV 682 ComprValueSE 4.591e-11 default compressibility fixed value for SV 682 ComprChoiceSV 0 default compressibility choice for SV 682 ComprValueSV 4.591e-11 default compressibility fixed value for SV 682 reportOutput TRUE FALSE RTF TRUE Report file: produce multi-fits textType numberSeq minOutput TRUE FALSE GPerL TRUE Minimum file: produce brief concUnits numberSeq concROutput FALSE UNUSED MolPerL UNUSED 0 99 Conc(r) file: produce [unused] concUnits [unused] r0 r1 freq concTOutput FALSE UNUSED MolPerL UNUSED Conc(t) file: produce [unused] concUnits logsOutput UNUSED 5 Log files: unused produceLogs minScanPairPrint 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 which scan pairs to print (start,end,show,skip)