Changeset 920


Ignore:
Timestamp:
Apr 13, 2020 8:59:02 PM (2 years ago)
Author:
ilavsky
Message:

WIP

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/User Procedures/Irena/IRB1_bioSAXS.ipf

    r919 r920  
    15541554        //here we need some output values from GNOM, need space at leats for Alfa
    15551555        SetVariable GNOMAlfaResult,pos={270,400},size={160,15}, noproc,title="GNOM Alfa out =",variable=root:Packages:Irena:PDDFInterface:GNOMAlfaResult,disable=0, noedit=1,limits={0,inf,0},frame=0
    1556         TitleBox PDDFInstructions2 title="\Zr120MW estimate requires Absolute Intensity!",size={330,15},pos={270,420},frame=0,fColor=(0,0,65535),labelBack=0
    1557         SetVariable ConcentrationForCals,pos={270,440},size={220,15}, proc=IRB1_PDDFSetVarProc,title="c [mg/ml] =              ",variable=root:Packages:Irena:PDDFInterface:ConcentrationForCals,limits={0,inf,0.1}, help={"Concentration for MW calculations"}
    15581556
    15591557        //TAB 1
    15601558        //MW controls
    1561         TitleBox PDDFInstructions1 title="\Zr120SAXSMoW2 MW Calc : ",size={230,15},pos={270,156},frame=0,fColor=(0,0,65535),labelBack=0
    1562         checkbox PDDFUseProtein, pos={300,180}, title="\Zr120Protein", size={120,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:PDDFUseProtein, fColor=(65535,0,0), mode=1, help={"Run PDDF with setting for Proteins. Changes density and SLD"}
    1563         checkbox PDDFUseNucleicAcid, pos={450,180}, title="\Zr120Nucleic Acid", size={120,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:PDDFUseNucleicAcid, fColor=(65535,0,0), mode=1, help={"Run PDDF with settings from Nucleai acid. Changes density and SLD"}
    1564         Button CalcRgAndMolecularWeight,pos={310,210},size={170,20}, proc=IRB1_PDDFButtonProc,title="Fit Rg and calculate MW", help={"Calculate Dmax on these data"}
     1559        checkbox PDDFUseProtein, pos={300,155}, title="\Zr120Protein", size={120,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:PDDFUseProtein, fColor=(65535,0,0), mode=1, help={"Run PDDF with setting for Proteins. Changes density and SLD"}
     1560        checkbox PDDFUseNucleicAcid, pos={450,155}, title="\Zr120Nucleic Acid", size={120,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:PDDFUseNucleicAcid, fColor=(65535,0,0), mode=1, help={"Run PDDF with settings from Nucleai acid. Changes density and SLD"}
     1561        Button CalcRgAndMolecularWeight,pos={310,180},size={170,20}, proc=IRB1_PDDFButtonProc,title="Fit Rg and calculate MW", help={"Calculate Dmax on these data"}
     1562        TitleBox PDDFInstructions1 title="\Zr120SAXSMoW2 & Rambo-Tainer Qmax : ",size={230,15},pos={270,220},frame=0,fColor=(0,0,65535),labelBack=0
    15651563        checkbox RamboTainerQmax8overRg, pos={270,250}, title="Qmax 8/Rg?", size={76,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:RamboTainerQmax8overRg, mode=0, help={"Set Qmax to 8/Rg automatically"}
    15661564        checkbox RamboTainerQmaxLog225, pos={400,250}, title="Qmax I(0)/200?", size={76,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:RamboTainerQmaxLog225, mode=0, help={"Set Qmax to Q when I(0)/200"}
    1567         SetVariable RamboTainerQmax,pos={260,275},size={250,15}, proc=IRB1_PDDFSetVarProc,title="Qmax = ", variable=root:Packages:Irena:PDDFInterface:RamboTainerQmax, limits={0.01,1,0.1},frame=1,bodyWidth=90, help={"Qmax to use"}, format="%4.2f"
    1568 
    1569 
    1570         checkbox RamboTainerAutoSetBckg, pos={270,300}, title="Auto Find Background?", size={76,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:RamboTainerAutoSetBckg, mode=0, help={"Find Background AUtomatically background from I(Q)"}
    1571         checkbox RamboTainerSubtractFlatBackground, pos={270,325}, title="Subtract Background?", size={76,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:RamboTainerSubtractFlatBackground, mode=0, help={"Subtract background from I(Q)"}
    1572         SetVariable RamboTainerFlatBackground,pos={260,350},size={250,17}, bodyWidth=90, proc=IRB1_PDDFSetVarProc,title="Flat Background = ", variable=root:Packages:Irena:PDDFInterface:RamboTainerFlatBackground, limits={0.01,1,0.02},frame=1, help={"Flat Background"}, format="%4.2f"
    1573 
    1574         SetVariable MWTrueVolumeA3,pos={270,420},size={250,15}, noproc,title="Porod Volume [A^3] =  ", variable=root:Packages:Irena:PDDFInterface:MWTrueVolumeA3, noedit=1,limits={0,inf,0},frame=0, help={"True Volume of protein in [cm3] "}
    1575 
     1565        SetVariable RamboTainerQmax,pos={270,275},size={250,18}, bodyWidth=90, proc=IRB1_PDDFSetVarProc,title="Qmax = ", variable=root:Packages:Irena:PDDFInterface:RamboTainerQmax, limits={0.01,1,0.1},frame=1,bodyWidth=90, help={"Qmax to use"}, format="%4.2f"
     1566
     1567        TitleBox PDDFInstructions11 title="\Zr120Rambo-Tainer Background : ",size={230,15},pos={270,310},frame=0,fColor=(0,0,65535),labelBack=0
     1568        checkbox RamboTainerAutoSetBckg, pos={270,330}, title="Auto Find Backg.?", size={76,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:RamboTainerAutoSetBckg, mode=0, help={"Find Background AUtomatically background from I(Q)"}
     1569        checkbox RamboTainerSubtractFlatBackground, pos={420,330}, title="Subtract Background?", size={76,14},proc=IRB1_PDDFCheckProc, variable=root:Packages:Irena:PDDFInterface:RamboTainerSubtractFlatBackground, mode=0, help={"Subtract background from I(Q)"}
     1570        SetVariable RamboTainerFlatBackground,pos={270,355},size={250,18}, bodyWidth=90, proc=IRB1_PDDFSetVarProc,title="Flat Background = ", variable=root:Packages:Irena:PDDFInterface:RamboTainerFlatBackground, limits={0.01,1,0.02},frame=1, help={"Flat Background"}, format="%4.2f"
     1571
     1572        TitleBox PDDFInstructions12 title="\Zr120Real Space/PDDF (GNOM) Mol. Weight Conc.",size={330,15},pos={270,390},frame=0,fColor=(0,0,65535),labelBack=0
     1573        SetVariable ConcentrationForCals,pos={270,410},size={250,18}, proc=IRB1_PDDFSetVarProc,title="c [mg/ml] = ", bodyWidth=90,variable=root:Packages:Irena:PDDFInterface:ConcentrationForCals,limits={0,inf,0.1}, help={"Concentration for MW calculations"}
     1574        TitleBox PDDFInstructions2 title="\Zr100Remember - this Estimate requires Absolute Intensity!",size={330,15},pos={270,435},frame=0,fColor=(0,0,65535),labelBack=0
    15761575
    15771576
     
    15801579        //GNOM calculated results
    15811580        TitleBox PDDFInstructions21 title="\Zr120Results :",size={330,15},pos={270,475},frame=0,fColor=(0,0,65535),labelBack=0
    1582         SetVariable SAXSMoW2I0,pos={260,500},size={200,15}, noproc,title="SAXSMoW2 I0 =   ", variable=root:Packages:Irena:PDDFInterface:SAXSMoW2I0, noedit=1,limits={0,inf,0},frame=0,size={180,17}, bodyWidth=70, help={"Porod Invariant calcualtion result"}, format="%4.2f"
    1583         SetVariable SAXSMoW2Rg,pos={470,500},size={120,17},bodyWidth=70, noproc,title="Rg [A]  = ", variable=root:Packages:Irena:PDDFInterface:SAXSMoW2Rg, noedit=1,limits={0,inf,0},frame=0, help={"Density of protein, user changeable, in g/cm3"}, format="%4.2f"
    1584         SetVariable MWMolecularWeightkDa,pos={300,520},size={250,15},bodyWidth=70, noproc,title="SAXSMoW2 MW [kDa]  =  ", variable=root:Packages:Irena:PDDFInterface:MWMolecularWeightkDa, noedit=1,fstyle=1, fsize=13, limits={0,inf,0},frame=0, help={"Molecular weight calculated from SAXSMoW2 method in kDa"}, fColor=(52428,1,1), format="%8.2f"
    1585         SetVariable RamboTainerMW,pos={300,550},size={250,15},bodyWidth=70, noproc,title="Rambo-Tainer MW [kDa] = ",variable=root:Packages:Irena:PDDFInterface:RamboTainerMW, disable=0, noedit=1,limits={0,inf,0},frame=0,fstyle=1, fsize=13, fColor=(52428,1,1), help={"Molecular weight calculated from Rambo-Tainer method in kDa"}, format="%8.2f"
    1586        
    1587         SetVariable PDDFCalculatedI0,pos={260,590},size={200,15}, noproc,title="PDDF I0 =   ",variable=root:Packages:Irena:PDDFInterface:PDDFCalculatedI0, disable=0, noedit=1,limits={0,inf,0},frame=0, size={180,17}, bodyWidth=70, help={"Porod Invariant calcualtion result"}, format="%4.2f"
    1588         SetVariable PDDFCalculatedRg,pos={470,590},size={120,17},bodyWidth=70, noproc,title="Rg [A] =     ",variable=root:Packages:Irena:PDDFInterface:PDDFCalculatedRg,  disable=0, noedit=1,limits={0,inf,0},frame=0, format="%4.2f"
    1589         SetVariable PDDFCalculatedMW,pos={300,620},size={250,15},bodyWidth=70, noproc,title="PDDF MW [kDa] = ",variable=root:Packages:Irena:PDDFInterface:PDDFCalculatedMW, disable=0, noedit=1,limits={0,inf,0},frame=0,fstyle=1, fsize=13, fColor=(52428,1,1), help={"Molecular weight calculated from PDDF method in kDa"}, format="%8.2f"
     1581        SetVariable MWTrueVolumeA3,pos={400,475},size={250,15}, noproc,title="Porod Volume [A^3] =  ", variable=root:Packages:Irena:PDDFInterface:MWTrueVolumeA3, noedit=1,limits={0,inf,0},frame=0, help={"True Volume of protein in [cm3] "}
     1582
     1583        SetVariable ReciprocalSpaceI0,pos={260,500},size={200,15}, noproc,title="Reciprocal Space I0 =   ", variable=root:Packages:Irena:PDDFInterface:ReciprocalSpaceI0, noedit=1,limits={0,inf,0},frame=0,size={180,17}, bodyWidth=70, help={"Porod Invariant calcualtion result"}, format="%4.2f"
     1584        SetVariable ReciprocalSpaceRg,pos={470,500},size={120,17},bodyWidth=70, noproc,title="Rg [A]  = ", variable=root:Packages:Irena:PDDFInterface:ReciprocalSpaceRg, noedit=1,limits={0,inf,0},frame=0, help={"Density of protein, user changeable, in g/cm3"}, format="%4.2f"
     1585        SetVariable SAXSMoW2MWRecSpacekDa,pos={300,520},size={250,15},bodyWidth=70, noproc,title="SAXSMoW2 MW [kDa]  = ", variable=root:Packages:Irena:PDDFInterface:SAXSMoW2MWRecSpacekDa, noedit=1,fstyle=1, fsize=13, limits={0,inf,0},frame=0, help={"Molecular weight calculated from SAXSMoW2 method in kDa"}, fColor=(52428,1,1), format="%8.2f"
     1586        SetVariable RamboTainerMW,pos={300,545},size={250,15},bodyWidth=70, noproc,title="Rambo-Tainer MW [kDa]  = ",variable=root:Packages:Irena:PDDFInterface:RamboTainerMW, disable=0, noedit=1,limits={0,inf,0},frame=0,fstyle=1, fsize=13, fColor=(52428,1,1), help={"Molecular weight calculated from Rambo-Tainer method in kDa"}, format="%8.2f"
     1587       
     1588        SetVariable RealSpaceI0,pos={260,580},size={200,15}, noproc,title="Real Space (GNOM) I0 = ",variable=root:Packages:Irena:PDDFInterface:RealSpaceI0, disable=0, noedit=1,limits={0,inf,0},frame=0, size={180,17}, bodyWidth=70, help={"Porod Invariant calcualtion result"}, format="%4.2f"
     1589        SetVariable RealSpaceRg,pos={470,580},size={120,17},bodyWidth=70, noproc,title="Rg [A] =     ",variable=root:Packages:Irena:PDDFInterface:RealSpaceRg,  disable=0, noedit=1,limits={0,inf,0},frame=0, format="%4.2f"
     1590        SetVariable SAXSMoW2MWRealSpacekDa,pos={300,605},size={250,15},bodyWidth=70, noproc,title="SAXSMoW2 MW [kDa]  = ", variable=root:Packages:Irena:PDDFInterface:SAXSMoW2MWRealSpacekDa, noedit=1,fstyle=1, fsize=13, limits={0,inf,0},frame=0, help={"Molecular weight calculated from SAXSMoW2 method in kDa"}, fColor=(52428,1,1), format="%8.2f"
     1591        SetVariable PDDFCalculatedMW,pos={300,630},size={250,15},bodyWidth=70, noproc,title="Abs. Int. Est. MW [kDa]  = ",variable=root:Packages:Irena:PDDFInterface:PDDFCalculatedMW, disable=0, noedit=1,limits={0,inf,0},frame=0,fstyle=1, fsize=13, fColor=(52428,1,1), help={"Molecular weight calculated from PDDF method in kDa"}, format="%8.2f"
    15901592
    15911593
     
    16391641                       
    16401642                        NVAR RamboTainerQmax = root:Packages:Irena:PDDFInterface:RamboTainerQmax
    1641                         NVAR SAXSMoW2Rg = root:Packages:Irena:PDDFInterface:SAXSMoW2Rg
    1642                         NVAR SAXSMoW2I0=root:Packages:Irena:PDDFInterface:SAXSMoW2I0
     1643                        NVAR ReciprocalSpaceRg = root:Packages:Irena:PDDFInterface:ReciprocalSpaceRg
     1644                        NVAR ReciprocalSpaceI0=root:Packages:Irena:PDDFInterface:ReciprocalSpaceI0
    16431645                        Wave Intensity=root:Packages:Irena:PDDFInterface:Intensity
    16441646                        Wave Qvector=root:Packages:Irena:PDDFInterface:Q_vec
    16451647                       
    1646                         if(RamboTainerQmax8overRg && SAXSMoW2Rg>0)     
    1647                                 RamboTainerQmax = 8/SAXSMoW2Rg
    1648                         elseif(RamboTainerQmaxLog225 && SAXSMoW2I0>0)
    1649                                 variable IntToFind = SAXSMoW2I0/200
     1648                        if(RamboTainerQmax8overRg && ReciprocalSpaceRg>0)       
     1649                                RamboTainerQmax = 8/ReciprocalSpaceRg
     1650                        elseif(RamboTainerQmaxLog225 && ReciprocalSpaceI0>0)
     1651                                variable IntToFind = ReciprocalSpaceI0/200
    16501652                                FindLevel/P/Q Intensity, IntToFind
    16511653                                if(V_Flag==0)   //level found...
     
    17701772        TitleBox PDDFInstructions1, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
    17711773        Button CalcRgAndMolecularWeight, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
    1772         SetVariable MWTrueVolumeA3, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
     1774        //SetVariable MWTrueVolumeA3, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
    17731775        checkbox RamboTainerAutoSetBckg,  disable = (whichTab!=1)
    17741776        checkbox RamboTainerQmax8overRg,  disable = (whichTab!=1)
     
    17771779        checkbox RamboTainerSubtractFlatBackground,  disable = (whichTab!=1)
    17781780        SetVariable RamboTainerFlatBackground,  disable = (whichTab!=1)
     1781        SetVariable ConcentrationForCals, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
     1782        TitleBox PDDFInstructions2, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
     1783        TitleBox PDDFInstructions11, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
     1784        TitleBox PDDFInstructions12, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=1)
    17791785        //PDDF Gnom specifics
    17801786        TitleBox PDDFInstructions5, win=IRB1_PDDFInterfacePanel,   disable = (whichTab!=0)
     
    17951801        checkbox MooreDetNumFunctions, win=IRB1_PDDFInterfacePanel, disable=(whichTab!=0 ||!PDDFuseMoore)
    17961802        checkbox MooreFitMaxSize, win=IRB1_PDDFInterfacePanel, disable=(whichTab!=0 ||!PDDFuseMoore)
    1797         TitleBox PDDFInstructions2, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=0)
    17981803        SetVariable DmaxEstimate, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=0)
    17991804        Button RunPDDFonData, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=0)
    18001805        Button RunSequenceofPDDF, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=0)
    18011806        SetVariable GNOMAlfaResult, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=0)
    1802         SetVariable ConcentrationForCals, win=IRB1_PDDFInterfacePanel,  disable = (whichTab!=0)
    18031807end
    18041808//**********************************************************************************************************
     
    19501954                        if(stringMatch(ba.ctrlName,"AutoScaleGraph"))
    19511955                                SetAxis/W=IRB1_PDDFInterfacePanel#DataDisplay /A
     1956                                SetAxis/W=IRB1_PDDFInterfacePanel#PDFDisplay /A
    19521957                        endif
    19531958                        if(stringmatch(ba.ctrlName,"GetHelp"))
     
    20282033Function IRB1_PDDFCalculateRgI0()
    20292034
    2030         NVAR CalcRg=root:Packages:Irena:PDDFInterface:PDDFCalculatedRg
    2031         NVAR CalcI0=root:Packages:Irena:PDDFInterface:PDDFCalculatedI0
     2035        NVAR CalcRg=root:Packages:Irena:PDDFInterface:RealSpaceRg
     2036        NVAR CalcI0=root:Packages:Irena:PDDFInterface:RealSpaceI0
    20322037        Wave Radius = root:Packages:Irena:PDDFInterface:pddfRadius
    20332038        Wave Pr = root:Packages:Irena:PDDFInterface:pddfPr
     
    21002105        //variable Background = w_coef[4]
    21012106        //these are globasl for them
    2102         NVAR SAXSMoW2I0=root:Packages:Irena:PDDFInterface:SAXSMoW2I0
    2103         NVAR SAXSMoW2Rg=root:Packages:Irena:PDDFInterface:SAXSMoW2Rg
    2104         SAXSMoW2I0 = G
    2105         SAXSMoW2Rg = Rg
     2107        NVAR ReciprocalSpaceI0=root:Packages:Irena:PDDFInterface:ReciprocalSpaceI0
     2108        NVAR ReciprocalSpaceRg=root:Packages:Irena:PDDFInterface:ReciprocalSpaceRg
     2109        ReciprocalSpaceI0 = G
     2110        ReciprocalSpaceRg = Rg
    21062111        //calculate Intensity to display
    21072112        Duplicate/O OriginalIntensity, QstarVector, FitScatteringProfile
     
    21292134        NVAR MWTrueVolumeA3=root:Packages:Irena:PDDFInterface:MWTrueVolumeA3
    21302135        NVAR MWMassDensityProtein=root:Packages:Irena:PDDFInterface:MWMassDensityProtein                        //g/cm3, see line after formula 11
    2131         NVAR MWMolecularWeightkDa=root:Packages:Irena:PDDFInterface:MWMolecularWeightkDa
     2136        NVAR SAXSMoW2MWRecSpacekDa=root:Packages:Irena:PDDFInterface:SAXSMoW2MWRecSpacekDa
    21322137        variable changeOverQmax = 8/Rg                                                                                                                                                  //formula 7
    21332138        //alternative is to pick changeOverQmax based on Formula 8, so log(I(o)/I(gmax) ~ 2.25, formula 7 is easier, keep for now...
     
    21502155        MWTrueVolumeA3  = Aval + Bval*Vprime                                                                                                            //this is in A^3
    21512156        //formula 11
    2152         MWMolecularWeightkDa = MWMassDensityProtein*MWTrueVolumeA3* 1e-24       /1.662e-21                     
     2157        SAXSMoW2MWRecSpacekDa = MWMassDensityProtein*MWTrueVolumeA3* 1e-24      /1.662e-21                     
    21532158        //this ends calculations for SAXSMoW2 ...
    21542159        //***
     
    22512256       
    22522257       
    2253         variable RTVc           =       SAXSMoW2I0/IntgQIQ
    2254         variable RTQr           =       (RTVc)^2 / SAXSMoW2Rg
     2258        variable RTVc           =       ReciprocalSpaceI0/IntgQIQ
     2259        variable RTQr           =       (RTVc)^2 / ReciprocalSpaceRg
    22552260        if(PDDFUseProtein)
    22562261                RamboTainerMW   =       (RTQr/0.1231)^1.0
     
    22642269        Tagtext+="\\F"+IN2G_LkUpDfltStr("FontType")+"\\Z"+IN2G_LkUpDfltVar("TagSize")+"I0 = "+num2str(G)
    22652270        //Tagtext+="\\F"+IN2G_LkUpDfltStr("FontType")+"\\Z"+IN2G_LkUpDfltVar("TagSize")+"Protein Vol [cm3] = "+num2str(MWTrueVolumeA3)+"\r"
    2266         Tagtext+="\\F"+IN2G_LkUpDfltStr("FontType")+"\\Z"+IN2G_LkUpDfltVar("TagSize")+"     MW [kDa] = "+num2str(MWMolecularWeightkDa)
     2271        Tagtext+="\\F"+IN2G_LkUpDfltStr("FontType")+"\\Z"+IN2G_LkUpDfltVar("TagSize")+"     MW [kDa] = "+num2str(SAXSMoW2MWRecSpacekDa)
    22672272        Tag/C/N=GuessRg/A=LT/L=0/TL=0/W=IRB1_PDDFInterfacePanel#DataDisplay FitScatteringProfile, numpnts(FitScatteringProfile)/10,Tagtext
    22682273       
     
    26042609        //read values from out file... 
    26052610        NVAR GNOMAlfaResult = root:Packages:Irena:PDDFInterface:GNOMAlfaResult
    2606         NVAR PDDFCalculatedRg = root:Packages:Irena:PDDFInterface:PDDFCalculatedRg
    2607         NVAR PDDFCalculatedI0 = root:Packages:Irena:PDDFInterface:PDDFCalculatedI0
     2611        NVAR RealSpaceRg = root:Packages:Irena:PDDFInterface:RealSpaceRg
     2612        NVAR RealSpaceI0 = root:Packages:Irena:PDDFInterface:RealSpaceI0
    26082613        make/Free/T/N=0 TempStrWave
    26092614        Grep /E="Current ALPHA:" GNOMOutFileTextWave as TempStrWave     
    26102615        GNOMAlfaResult = str2num(StringFromList(1, TempStrWave[0]+":", ":"))
    26112616        Grep /E="Real space Rg:" GNOMOutFileTextWave as TempStrWave     
    2612         PDDFCalculatedRg = str2num(StringFromList(1, TempStrWave[0]+":", ":"))
     2617        RealSpaceRg = str2num(StringFromList(1, TempStrWave[0]+":", ":"))
    26132618        Grep /E="Real space I" GNOMOutFileTextWave as TempStrWave       
    2614         PDDFCalculatedI0 = str2num(StringFromList(1, TempStrWave[0]+":", ":"))
     2619        RealSpaceI0 = str2num(StringFromList(1, TempStrWave[0]+":", ":"))
    26152620        print "***************************************************************************"
    26162621        For(i=0;i<60;i+=1)
     
    28262831        NVAR MWTrueVolumeA3 = root:Packages:Irena:PDDFInterface:MWTrueVolumeA3
    28272832        NVAR MWMassDensityProtein = root:Packages:Irena:PDDFInterface:MWMassDensityProtein
    2828         NVAR MWMolecularWeightkDa = root:Packages:Irena:PDDFInterface:MWMolecularWeightkDa
    2829         NVAR SAXSMoW2I0 = root:Packages:Irena:PDDFInterface:SAXSMoW2I0
    2830         NVAR SAXSMoW2Rg = root:Packages:Irena:PDDFInterface:SAXSMoW2Rg
     2833        NVAR SAXSMoW2MWRecSpacekDa = root:Packages:Irena:PDDFInterface:SAXSMoW2MWRecSpacekDa
     2834        NVAR ReciprocalSpaceI0 = root:Packages:Irena:PDDFInterface:ReciprocalSpaceI0
     2835        NVAR ReciprocalSpaceRg = root:Packages:Irena:PDDFInterface:ReciprocalSpaceRg
    28312836        MWPorodInvariant = 0
    28322837        MWTrueVolumeA3 = 0
    2833         MWMolecularWeightkDa = 0
    2834         SAXSMoW2I0 = 0
    2835         SAXSMoW2Rg = 0
    2836        
    2837         NVAR CalcRg=root:Packages:Irena:PDDFInterface:PDDFCalculatedRg
    2838         NVAR CalcI0=root:Packages:Irena:PDDFInterface:PDDFCalculatedI0
     2838        SAXSMoW2MWRecSpacekDa = 0
     2839        ReciprocalSpaceI0 = 0
     2840        ReciprocalSpaceRg = 0
     2841       
     2842        NVAR CalcRg=root:Packages:Irena:PDDFInterface:RealSpaceRg
     2843        NVAR CalcI0=root:Packages:Irena:PDDFInterface:RealSpaceI0
    28392844        NVAR ConcentrationForCals=root:Packages:Irena:PDDFInterface:ConcentrationForCals
    28402845        NVAR ScattLengthDensDifference=root:Packages:Irena:PDDFInterface:ScattLengthDensDifference
     
    30063011        ListOfVariables += "DmaxEstimate;CalculateDmaxEstOnImport;GnomForceRmin0;GnomForceRmax0;NumBinsInR;GnomAlfaValue;"     
    30073012        ListOfVariables += "MooreNumFunctions;MooreDetNumFunctions;MooreFitMaxSize;"   
    3008         ListOfVariables += "PDDFCalculatedRg;PDDFCalculatedI0;ConcentrationForCals;ScattLengthDensDifference;PDDFCalculatedMW;"
     3013        ListOfVariables += "RealSpaceRg;RealSpaceI0;ConcentrationForCals;ScattLengthDensDifference;PDDFCalculatedMW;"   
    30093014        ListOfVariables += "RamboTainerMW;RamboTainerQmax8overRg;RamboTainerQmax;RamboTainerQmaxLog225;"
    30103015        ListOfVariables += "RamboTainerSubtractFlatBackground;RamboTainerFlatBackground;RamboTainerAutoSetBckg;"
    30113016        ListOfVariables += "SaveToFolder;SaveToNotebook;SaveToWaves;SaveToGNOMOut;"     
    3012         ListOfVariables += "MWPorodInvariant;MWTrueVolumeA3;MWMassDensityProtein;MWMolecularWeightkDa;"
    3013         ListOfVariables += "GNOMAlfaResult;SAXSMoW2I0;SAXSMoW2Rg;PDDFUseProtein;PDDFUseNucleicAcid;"
     3017        ListOfVariables += "MWPorodInvariant;MWTrueVolumeA3;MWMassDensityProtein;SAXSMoW2MWRecSpacekDa;SAXSMoW2MWRealSpacekDa;"
     3018        ListOfVariables += "GNOMAlfaResult;ReciprocalSpaceI0;ReciprocalSpaceRg;PDDFUseProtein;PDDFUseNucleicAcid;"
    30143019
    30153020                //and here we create them
     
    30923097        NVAR MWTrueVolumeA3 = root:Packages:Irena:PDDFInterface:MWTrueVolumeA3
    30933098        NVAR MWMassDensityProtein = root:Packages:Irena:PDDFInterface:MWMassDensityProtein
    3094         NVAR MWMolecularWeightkDa = root:Packages:Irena:PDDFInterface:MWMolecularWeightkDa
    3095         NVAR SAXSMoW2I0 = root:Packages:Irena:PDDFInterface:SAXSMoW2I0
    3096         NVAR SAXSMoW2Rg = root:Packages:Irena:PDDFInterface:SAXSMoW2Rg
    3097         NVAR PDDFCalculatedRg = root:Packages:Irena:PDDFInterface:PDDFCalculatedRg
    3098         NVAR PDDFCalculatedI0 = root:Packages:Irena:PDDFInterface:PDDFCalculatedI0
     3099        NVAR SAXSMoW2MWRecSpacekDa = root:Packages:Irena:PDDFInterface:SAXSMoW2MWRecSpacekDa
     3100        NVAR ReciprocalSpaceI0 = root:Packages:Irena:PDDFInterface:ReciprocalSpaceI0
     3101        NVAR ReciprocalSpaceRg = root:Packages:Irena:PDDFInterface:ReciprocalSpaceRg
     3102        NVAR RealSpaceRg = root:Packages:Irena:PDDFInterface:RealSpaceRg
     3103        NVAR RealSpaceI0 = root:Packages:Irena:PDDFInterface:RealSpaceI0
    30993104        NVAR PDDFCalculatedMW = root:Packages:Irena:PDDFInterface:PDDFCalculatedMW
    31003105        NVAR GNOMAlfaResult=root:Packages:Irena:PDDFInterface:GNOMAlfaResult
     
    31043109        MWPorodInvariant = 0
    31053110        MWTrueVolumeA3 = 0
    3106         MWMolecularWeightkDa = 0
    3107         SAXSMoW2I0 = 0
    3108         SAXSMoW2Rg = 0
    3109         PDDFCalculatedRg=0
    3110         PDDFCalculatedI0=0
     3111        SAXSMoW2MWRecSpacekDa = 0
     3112        ReciprocalSpaceI0 = 0
     3113        ReciprocalSpaceRg = 0
     3114        RealSpaceRg=0
     3115        RealSpaceI0=0
    31113116        PDDFCalculatedMW=0
    31123117        GNOMAlfaResult = 0
     
    31633168        NVAR MWTrueVolumeA3 = root:Packages:Irena:PDDFInterface:MWTrueVolumeA3
    31643169        NVAR MWMassDensityProtein = root:Packages:Irena:PDDFInterface:MWMassDensityProtein
    3165         NVAR MWMolecularWeightkDa = root:Packages:Irena:PDDFInterface:MWMolecularWeightkDa
     3170        NVAR SAXSMoW2MWRecSpacekDa = root:Packages:Irena:PDDFInterface:SAXSMoW2MWRecSpacekDa
    31663171        NVAR GNOMAlfaResult = root:Packages:Irena:PDDFInterface:GNOMAlfaResult
    31673172
    3168         NVAR CalcRg=root:Packages:Irena:PDDFInterface:PDDFCalculatedRg
    3169         NVAR CalcI0=root:Packages:Irena:PDDFInterface:PDDFCalculatedI0
     3173        NVAR CalcRg=root:Packages:Irena:PDDFInterface:RealSpaceRg
     3174        NVAR CalcI0=root:Packages:Irena:PDDFInterface:RealSpaceI0
    31703175        NVAR ConcentrationForCals=root:Packages:Irena:PDDFInterface:ConcentrationForCals
    31713176        NVAR ScattLengthDensDifference=root:Packages:Irena:PDDFInterface:ScattLengthDensDifference
     
    32013206        IR1_AppendAnyText("PDDF SLD [10^10 cm^-2] = \t"+num2str(ScattLengthDensDifference),0)   
    32023207
    3203         IR1_AppendAnyText("\rPorod MW [kDa] = \t"+num2str(MWMolecularWeightkDa),0)     
     3208        IR1_AppendAnyText("\rPorod MW [kDa] = \t"+num2str(SAXSMoW2MWRecSpacekDa),0)     
    32043209        IR1_AppendAnyText("Porod Volume [cm3] = \t"+num2str(MWTrueVolumeA3),0) 
    32053210        IR1_AppendAnyText("Porod Density prot [g/cm3] = \t"+num2str(MWMassDensityProtein),0)   
     
    32413246        endif
    32423247
    3243         NVAR CalcRg=root:Packages:Irena:PDDFInterface:PDDFCalculatedRg
    3244         NVAR CalcI0=root:Packages:Irena:PDDFInterface:PDDFCalculatedI0
     3248        NVAR CalcRg=root:Packages:Irena:PDDFInterface:RealSpaceRg
     3249        NVAR CalcI0=root:Packages:Irena:PDDFInterface:RealSpaceI0
    32453250        NVAR ConcentrationForCals=root:Packages:Irena:PDDFInterface:ConcentrationForCals
    32463251        NVAR ScattLengthDensDifference=root:Packages:Irena:PDDFInterface:ScattLengthDensDifference
     
    32513256        NVAR MWTrueVolumeA3 = root:Packages:Irena:PDDFInterface:MWTrueVolumeA3
    32523257        NVAR MWMassDensityProtein = root:Packages:Irena:PDDFInterface:MWMassDensityProtein
    3253         NVAR MWMolecularWeightkDa = root:Packages:Irena:PDDFInterface:MWMolecularWeightkDa
     3258        NVAR SAXSMoW2MWRecSpacekDa = root:Packages:Irena:PDDFInterface:SAXSMoW2MWRecSpacekDa
    32543259        NVAR GNOMAlfaResult = root:Packages:Irena:PDDFInterface:GNOMAlfaResult
    32553260
     
    32953300        PorodTrueVolume[curlength] = MWTrueVolumeA3
    32963301        MassDensityProtein[curlength] = MWMassDensityProtein
    3297         InvariantPDDFCalculatedMW[curlength] = MWMolecularWeightkDa
     3302        InvariantPDDFCalculatedMW[curlength] = SAXSMoW2MWRecSpacekDa
    32983303        GnomAlfaFinal[curlength] = GNOMAlfaResult
    32993304        DoWindow IRB1_PDDFFitResultsTable
     
    33763381        NVAR MWTrueVolumeA3 = root:Packages:Irena:PDDFInterface:MWTrueVolumeA3
    33773382        NVAR MWMassDensityProtein = root:Packages:Irena:PDDFInterface:MWMassDensityProtein
    3378         NVAR MWMolecularWeightkDa = root:Packages:Irena:PDDFInterface:MWMolecularWeightkDa
     3383        NVAR SAXSMoW2MWRecSpacekDa = root:Packages:Irena:PDDFInterface:SAXSMoW2MWRecSpacekDa
    33793384        NVAR GNOMAlfaResult = root:Packages:Irena:PDDFInterface:GNOMAlfaResult
    33803385
    3381         NVAR CalcRg=root:Packages:Irena:PDDFInterface:PDDFCalculatedRg
    3382         NVAR CalcI0=root:Packages:Irena:PDDFInterface:PDDFCalculatedI0
     3386        NVAR CalcRg=root:Packages:Irena:PDDFInterface:RealSpaceRg
     3387        NVAR CalcI0=root:Packages:Irena:PDDFInterface:RealSpaceI0
    33833388        NVAR ConcentrationForCals=root:Packages:Irena:PDDFInterface:ConcentrationForCals
    33843389        NVAR ScattLengthDensDifference=root:Packages:Irena:PDDFInterface:ScattLengthDensDifference
     
    34093414        ResultsComment="PDDFSLD="+num2str(ScattLengthDensDifference)+";"
    34103415        ResultsComment="PDDFAlfaFinal="+num2str(GNOMAlfaResult)+";"
    3411         ResultsComment="PorodMW="+num2str(MWMolecularWeightkDa)+";"
     3416        ResultsComment="PorodMW="+num2str(SAXSMoW2MWRecSpacekDa)+";"
    34123417        ResultsComment="PorodInvariant="+num2str(MWPorodInvariant)+";"
    34133418        ResultsComment="PorodVolume="+num2str(MWTrueVolumeA3)+";"
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