(*********************************************************************** Mathematica-Compatible Notebook This notebook can be used on any computer system with Mathematica 3.0, MathReader 3.0, or any compatible application. The data for the notebook starts with the line of stars above. To get the notebook into a Mathematica-compatible application, do one of the following: * Save the data starting with the line of stars above into a file with a name ending in .nb, then open the file inside the application; * Copy the data starting with the line of stars above to the clipboard, then use the Paste menu command inside the application. Data for notebooks contains only printable 7-bit ASCII and can be sent directly in email or through ftp in text mode. Newlines can be CR, LF or CRLF (Unix, Macintosh or MS-DOS style). NOTE: If you modify the data for this notebook not in a Mathematica- compatible application, you must delete the line below containing the word CacheID, otherwise Mathematica-compatible applications may try to use invalid cache data. For more information on notebooks and Mathematica-compatible applications, contact Wolfram Research: web: http://www.wolfram.com email: info@wolfram.com phone: +1-217-398-0700 (U.S.) Notebook reader applications are available free of charge from Wolfram Research. ***********************************************************************) (*CacheID: 232*) (*NotebookFileLineBreakTest NotebookFileLineBreakTest*) (*NotebookOptionsPosition[ 31041, 1118]*) (*NotebookOutlinePosition[ 32094, 1152]*) (* CellTagsIndexPosition[ 32050, 1148]*) (*WindowFrame->Normal*) Notebook[{ Cell[CellGroupData[{ Cell[TextData[{ StyleBox["The Binding of Symmetric Ligands to an Infinite Linear Lattice", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"New York", FontSize->14], StyleBox[" \n", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"New York"], StyleBox["by Alan R. Wolfe", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Chicago", FontSize->12, FontWeight->"Plain", FontSlant->"Italic"] }], "Title", Editable->False, Evaluatable->False, TextAlignment->Center, AspectRatioFixed->True, FontFamily->"New York", FontSize->14], Cell[TextData[{ StyleBox["This ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["Mathematica", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[ " notebook calculates and plots the Scatchard plot, neighbor-effect \ parameter, conditional probabilities, and cluster length distribution for \ the symmetric ligand case. It also permits comparison of an experimental \ Scatchard plot with the calculated theoretical data. It can only be used \ after the appropriate initialization notebook has been evaluated. To perform \ the calculations, simply set the input variables to the desired values and \ execute the ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["\"Kernel-> Evaluation-> Evaluate Notebook\"", FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[ " command. This may be repeated with different values for the input \ variables. \n\nThe notebook may also be executed in sections. To operate in \ this manner, the input parameters cell (as well as the experimental data \ cell, if desired) must be executed first. Then, if you want to plot the \ Scatchard plot, neighbor-effect parameter, or any of the conditional \ probabilities, the cell immediately below the first \"Calculate\[Ellipsis]\" \ heading must be executed next, followed by the desired output. In this \ case, it's easiest to start by simply selecting the right-most cell grouping \ bracket and executing everything from the input parameters to the Scatchard \ plot. If you want any of the 3-D cluster length plots, after the input \ parameters cell skip directly to the cell immediately below the second \ \"Calculate\[Ellipsis]\" heading, followed by the desired 3-D plot. If you \ want any of the 2-D cluster length plots, after the input parameters cell \ skip directly to the cell immediately below the third \ \"Calculate\[Ellipsis]\" heading, followed by the desired 2-D plot. (Note - \ the \"Iso\" and \"Ani\" programs cannot be excuted in the same manner; they \ require that the first calculation cell always be excuted before the second \ or third.) \n\nThe initial value of ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["experimentalrLf", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[" (= experimental r/[free ligand]) must be positive, and ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["experimentalData", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[ " must be True, in order to perform the experimental vs. theoretical \ comparison. If ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["experimentalData", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[" is False, only theoretical data will be generated (over n = ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["points", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[" equal intervals on the r axis). If ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["experimentalData", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[" is True, and the initial value of ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["experimentalrLf", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[ " is negative, again only theoretical data will be generated, but this time \ using the list of experimental r values provided (", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["rExpArray", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox["). ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]] }], "Text", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold"] }, Closed]], Cell[CellGroupData[{ Cell[TextData[StyleBox["INPUT VARIABLES: ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSize->10, FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}]], "Subsection", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["points = 10; k = 2; n = 2; w = 3; experimentalData = True; \n", AspectRatioFixed->True, FontColor->RGBColor[1, 0, 0]], StyleBox["(*", AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["variables for cluster length plots: *)", AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[ "\nrCluster2D = 0.9; maxLength2D = 6; \npoints3D = 10; maxLength3D = 5; ", AspectRatioFixed->True, FontColor->RGBColor[1, 0, 0]] }], "Input", AspectRatioFixed->True, FontFamily->"New York", FontColor->RGBColor[1, 0, 0]], Cell[TextData[{ StyleBox["rCluster2D", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[" * ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["rSat", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[ " is the r value for which 2D cluster length distribution data will be \ displayed. \n", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["points3D", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[ " is the number of equally spaced r values greater than zero for which the \ cluster length distribution will be displayed in the 3D plots. \n", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["maxLength", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[" is the maximum cluster length that will be considered. ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva"] }, Closed]], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["Experimental Data", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSize->10, FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox[" ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSize->12, FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["(* disregarded if experimentalData is False *)", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSize->10, FontColor->RGBColor[0, 0, 1]] }], "Subsection", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell[TextData[{ StyleBox["(* experimental r values - x values of most plots *)", Evaluatable->True, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Evaluatable->True, AspectRatioFixed->True, FontFamily->"Geneva", FontWeight->"Bold", FontColor->RGBColor[1, 0, 0]], StyleBox[ "\nrExpArray = {0.04, 0.05, 0.06, 0.12, 0.18, 0.30, 0.36, 0.42, 0.425} ; ", Evaluatable->True, AspectRatioFixed->True, FontWeight->"Bold", FontColor->RGBColor[1, 0, 0]] }], "Output", Editable->False, CellEditDuplicate->False, Evaluatable->True, GeneratedCell->False, CellAutoOverwrite->False, AspectRatioFixed->True, FontFamily->"New York"], Cell[TextData[StyleBox[ "(* The number of points in the two arrays must be equal. Also, neither \ array should have values corresponding to an empty or saturated lattice. *)", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell[TextData[{ StyleBox[ "(* experimental r/[free ligand] values - y values of Scatchard plot. \ These will be disregarded if the first value is negative *)", AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0]], StyleBox[ "\nexperimentalrLf = {2.02, 2.2, 2.05, 2.0, 1.96, 1.37, 1.21, 0.6, 0.61} ; \ ", AspectRatioFixed->True, FontColor->RGBColor[1, 0, 0]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"New York"] }, Closed]], Cell[TextData[StyleBox[ "Print [ \" initial slope = \", initialSlope //N ] ; ", Editable->False, CellOpen->False, AspectRatioFixed->True]], "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["(*", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["Calculate the NE parameter and Scatchard plot *) ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["scroll = 1 ", Editable->False, AspectRatioFixed->True, FontSize->9, FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell[TextData[{ StyleBox[ "(* Choose expression for neighbor-effect parameter and determine value of \ rSat *) ", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["\n", Editable->False, CellOpen->False, AspectRatioFixed->True], StyleBox["ne ; \nrSatDetermine ; \n\n", Editable->False, CellOpen->False, AspectRatioFixed->True, FontWeight->"Plain"], StyleBox["(* Initialize output arrays *)", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["\n", Editable->False, CellOpen->False, AspectRatioFixed->True, FontColor->RGBColor[0, 0, 1]], StyleBox[ "If [ experimentalrLf[[1]]<0, useData=False, useData=True ] ; \nIf [ \ experimentalData==False, \n points2 = points ; \n xAxisInterval = \ rSat/(points2) ; \n abscissa = Range [0, points2-1] ; abscissa2 = {} ; \n \ points4 = points2 ; \n", Editable->False, CellOpen->False, AspectRatioFixed->True, FontWeight->"Plain"], StyleBox[ " AppendTo [ abscissa2, points4 - 1/2] ; points2 = points2+1 ;\n \ AppendTo [ abscissa2, points4 - 1/4] ; points2 = points2+1 ;\n", Editable->False, CellOpen->False, AspectRatioFixed->True, FontColor->RGBColor[1, 0, 1]], StyleBox[" ", Editable->False, CellOpen->False, AspectRatioFixed->True, FontWeight->"Plain", FontColor->GrayLevel[0.666667]], StyleBox[ "abscissa = xAxisInterval Join [ abscissa, abscissa2 ] ] ; \nIf [ \ experimentalData==True, \n abscissa = Prepend [ rExpArray, 0 ] ; \n \ points2 = Length [ abscissa ] ; \n Do [ \n If [ abscissa[[i]] \ >= rSat, abscissa = Drop [ abscissa, {i,i} ] ], \n {i, points2, 1, \ -1} ] ; \n points2 = Length [ abscissa ] ; \n experimentalrLf = Take \ [ experimentalrLf, points2-1 ] ] ; \n \n", Editable->False, CellOpen->False, AspectRatioFixed->True, FontWeight->"Plain"], StyleBox["(* Evaluate the neighbor-effect parameter *)", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["\n", Editable->False, CellOpen->False, AspectRatioFixed->True, FontColor->RGBColor[0, 0, 1]], StyleBox[ "ordinate = Map [ Function [ zz, r = zz ; x = r/(1 - n r) ; \n {rLf, e, \ x, ff} ], abscissa ] ; \nAppendTo [ abscissa, rSat ] ; \nAppendTo [ ordinate, \ {0, w, 0, 0} ] ; ", Editable->False, CellOpen->False, AspectRatioFixed->True, FontWeight->"Plain"] }], "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["(*", Editable->False, AspectRatioFixed->True, FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, AspectRatioFixed->True, FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["Display the Scatchard plot *) ", Editable->False, AspectRatioFixed->True, FontColor->RGBColor[0, 0, 1]], StyleBox["scroll = 1 ", Editable->False, AspectRatioFixed->True, FontSize->9, FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ If [ experimentalData && useData, makePlot2 , makePlot [ 1, 0, \"r/Lf\", \"Scatchard plot\" ] ] \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"], Cell["\<\ If [ experimentalData && useData, theoreticalrLf = Table [ ordinate[[i,1]], {i,2,points2} ] ; Print [ \"correlation coefficient (R) = \", corrCoeff [ experimentalrLf, theoreticalrLf ] ] ; makeResidualsPlot [ experimentalrLf, theoreticalrLf ] ] \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"], Cell["\<\ If [ experimentalData && useData, makeResidualsPlot2 [ experimentalrLf, theoreticalrLf ] ] ; \ \>", "Input",\ Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["(*", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["Plot the neighbor-effect parameter *) ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["scroll = 1 ", Editable->False, AspectRatioFixed->True, FontSize->9, FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["makePlot [ 2, 1, \"e\", \"neighbor-effect\" ] ", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["(*", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["Plot the conditional probabilities *) ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["scroll = 1 ", Editable->False, AspectRatioFixed->True, FontSize->9, FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* ff *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["makePlot [ 4, 0, \"ff\", \"\" ] ", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* bf *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["makeCPplot [ bf, \" bf\" ] ", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* fb *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["makeCPplot [ fb, \" fb\" ] ", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* bb *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["makeCPplot [ bb, \" bb\" ] ", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["(*", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["Calculate, print and plot 3D cluster length data *) ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["scroll = 1 ", Editable->False, AspectRatioFixed->True, FontSize->9, FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell[TextData[{ StyleBox["ne ; rSatDetermine ; ", Editable->False, CellOpen->False, AspectRatioFixed->True], "\nmaxLength = maxLength3D ; \nclusterArray = Table [ 0, {maxLength} ] ; \n\ ligandArray = clusterArray ; \nclusterArray3D = Table [ clusterArray, \ {points3D+1} ] ; \nligandArray3D = clusterArray3D ; \nclusterLengthArray = \ Range [1, maxLength ] ; \nprintHeadings ; \nDo [ rCluster = (ij/points3D) ; \ clusterDistribution ; \n clusterArray3D[[ij+1]] = clusterArray ; \n \ ligandArray3D[[ij+1]] = ligandArray , \n{ ij, 0, points3D} ] ; \nchooseTicks \ ; " }], "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* plot fraction of clusters, left view *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ threeDplot [ 2.2, -2.4, 1.0, \"length \", \" \ r/rSat\", \"f clus.\", clusterArray3D, tickArray1 ] ; \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* plot fraction of clusters, right view *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ threeDplot [ 2.2, 2.4, 1.0, \" length\", \"r/rSat \ \", \"f clus.\", clusterArray3D, tickArray0 ] ; \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* plot fraction of clusters, center view *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ threeDplot [ 2.2, -0.001, 1.0, \" length\", \"r/rSat\", \"f clus.\", clusterArray3D, tickArray ] ; \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* plot fraction of ligands, left view *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ threeDplot [ 2.2, -2.4, 1.0, \"length \", \" \ r/rSat\", \"f lig.\", ligandArray3D, tickArray1 ] ; \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* plot fraction of ligands, right view *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ threeDplot [ 2.2, 2.4, 1.0, \" length\", \"r/rSat \ \", \"f lig.\", ligandArray3D, tickArray0 ] ; \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]], Cell[CellGroupData[{ Cell[TextData[StyleBox["(* plot fraction of ligands, center view *)", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]]], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ threeDplot [ 2.2, -0.001, 1.0, \" length\", \"r/rSat\", \"f lig.\", ligandArray3D, tickArray ] ; \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["(*", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["Calculate, print and plot 2D cluster length data *) ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["scroll = 1 ", Editable->False, AspectRatioFixed->True, FontSize->9, FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell[TextData[{ StyleBox["ne ; rSatDetermine ; ", Editable->False, CellOpen->False, AspectRatioFixed->True], "\nrCluster = rCluster2D ; \nmaxLength = maxLength2D ; \nclusterArray = \ Table [ 0, {maxLength} ] ; \nligandArray = clusterArray ; \n\ clusterLengthArray = Range [1, maxLength ] ; \nprintHeadings ; \n\ clusterDistribution ; \nPrint [ \" \" ] ; \nPrint [ \"r = \", r, \"; average \ cluster length = \" , averageClusterLength ] ; \nPrint [ \"bb = \", \ bbCLUSTER, \"; bf = \", bfCluster ] ; \nPrint [ \"rCluster2D = \", \ rCluster2D, \n \"; maxLength2D = \", maxLength2D ] ; " }], "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"], Cell[CellGroupData[{ Cell[TextData[{ StyleBox["(*", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[1, 0, 0], FontVariations->{"Shadow"->True}], StyleBox["Plot 2D cluster length data *) ", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["scroll = 1 ", Editable->False, AspectRatioFixed->True, FontSize->9, FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, AspectRatioFixed->True, FontFamily->"Geneva"], Cell["\<\ twoDplot [ \"fraction clusters\", maxClusters, clusterArray ] ; \ \ \>", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"], Cell["twoDplot [ \"fraction ligands\", maxLigands, ligandArray ] ; ", "Input", Editable->False, CellOpen->False, AspectRatioFixed->True, FontFamily->"New York", FontWeight->"Plain"] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell["rCluster2D = 0.99; maxLength2D = 7; ", "Input", AspectRatioFixed->True, FontFamily->"New York", FontColor->RGBColor[1, 0, 0]], Cell[TextData[{ StyleBox["Note - if the values of ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["rCluster2D", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[" (= r/rSat) and/or ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox["maxLength2D", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontSlant->"Italic", FontColor->RGBColor[0, 0, 1]], StyleBox[ " are changed and the cell assigning these values is executed, the cluster \ length distribution can be recalculated for the new value(s) by selecting", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva", FontColor->RGBColor[0, 0, 1]], StyleBox[" ", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontColor->RGBColor[0, 0, 1]], StyleBox[ "and executing the group of cells above this group. (The selection is \ executed by hitting the \"shift-return\" keys or the \"enter\" key.) ", FontColor->RGBColor[0, 0, 1]] }], "Input", Editable->False, Evaluatable->False, AspectRatioFixed->True, FontFamily->"Geneva"] }, Open ]] }, FrontEndVersion->"Macintosh 3.0", ScreenRectangle->{{0, 640}, {0, 460}}, WindowToolbars->{}, CellGrouping->Manual, WindowSize->{546, 389}, WindowMargins->{{25, Automatic}, {18, Automatic}}, PrivateNotebookOptions->{"ColorPalette"->{RGBColor, -1}}, ShowCellLabel->True, ShowCellTags->False, RenderingOptions->{"ObjectDithering"->True, "RasterDithering"->False}, MacintoshSystemPageSetup->"\<\ 00<0001804P000000]P2:?oQon82n@960dL5:0?l0080001804P000000]P2:001 0000I00000400`<300000BL?00400@0000000000000006P801T1T00000000000 00000000000000000000000000000000\>" ] (*********************************************************************** Cached data follows. If you edit this Notebook file directly, not using Mathematica, you must remove the line containing CacheID at the top of the file. The cache data will then be recreated when you save this file from within Mathematica. ***********************************************************************) (*CellTagsOutline CellTagsIndex->{} *) (*CellTagsIndex CellTagsIndex->{} *) (*NotebookFileOutline Notebook[{ Cell[CellGroupData[{ Cell[1731, 51, 678, 26, 115, "Title", Evaluatable->False], Cell[2412, 79, 5615, 161, 679, "Text", Evaluatable->False] }, Closed]], Cell[CellGroupData[{ Cell[8064, 245, 325, 11, 29, "Subsection", Evaluatable->False], Cell[CellGroupData[{ Cell[8414, 260, 793, 24, 83, "Input"], Cell[9210, 286, 1734, 61, 114, "Input", Evaluatable->False] }, Closed]], Cell[CellGroupData[{ Cell[10981, 352, 764, 28, 32, "Subsection", Evaluatable->False], Cell[11748, 382, 755, 26, 46, "Output", Evaluatable->True], Cell[12506, 410, 401, 11, 63, "Input", Evaluatable->False], Cell[12910, 423, 598, 19, 63, "Input"] }, Closed]], Cell[13523, 445, 270, 9, 19, "Input", CellOpen->False], Cell[CellGroupData[{ Cell[13818, 458, 689, 25, 32, "Input"], Cell[14510, 485, 2789, 85, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[17336, 575, 592, 22, 32, "Input"], Cell[17931, 599, 246, 9, 19, "Input", CellOpen->False], Cell[18180, 610, 411, 11, 19, "Input", CellOpen->False], Cell[18594, 623, 239, 9, 19, "Input", CellOpen->False] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell[18882, 638, 678, 25, 32, "Input"], Cell[19563, 665, 176, 5, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[19776, 675, 678, 25, 32, "Input"], Cell[CellGroupData[{ Cell[20479, 704, 215, 7, 29, "Input"], Cell[20697, 713, 162, 5, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[20896, 723, 215, 7, 29, "Input"], Cell[21114, 732, 159, 5, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[21310, 742, 215, 7, 29, "Input"], Cell[21528, 751, 159, 5, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[21724, 761, 215, 7, 29, "Input"], Cell[21942, 770, 160, 5, 19, "Input", CellOpen->False] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell[22151, 781, 691, 25, 32, "Input"], Cell[22845, 808, 715, 17, 19, "Input", CellOpen->False], Cell[CellGroupData[{ Cell[23585, 829, 249, 7, 29, "Input"], Cell[23837, 838, 262, 9, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[24136, 852, 250, 7, 29, "Input"], Cell[24389, 861, 261, 9, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[24687, 875, 251, 7, 29, "Input"], Cell[24941, 884, 247, 8, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[25225, 897, 248, 7, 29, "Input"], Cell[25476, 906, 260, 9, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[25773, 920, 249, 7, 29, "Input"], Cell[26025, 929, 259, 9, 19, "Input", CellOpen->False] }, Open ]], Cell[CellGroupData[{ Cell[26321, 943, 250, 7, 29, "Input"], Cell[26574, 952, 245, 8, 19, "Input", CellOpen->False] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell[26868, 966, 691, 25, 32, "Input"], Cell[27562, 993, 731, 17, 19, "Input", CellOpen->False], Cell[CellGroupData[{ Cell[28318, 1014, 670, 25, 32, "Input"], Cell[28991, 1041, 204, 8, 19, "Input", CellOpen->False], Cell[29198, 1051, 191, 5, 19, "Input", CellOpen->False] }, Open ]] }, Open ]], Cell[CellGroupData[{ Cell[29438, 1062, 137, 3, 29, "Input"], Cell[29578, 1067, 1447, 48, 114, "Input", Evaluatable->False] }, Open ]] } ] *) (*********************************************************************** End of Mathematica Notebook file. ***********************************************************************)