= Lecture 3 =

== Supplementary files on enzyme fitting ==

 Create a directory ''Enzymes'' and download the following files into it:
  1. [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/Utilities/enzfitter.gnu|enzfitter.gnu]] and its data file [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/Utilities/enz1.dat|enz1.dat]].
  1. If you have Excel, the spreadsheet [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/Utilities/Enzfitter.xls|EnzFitter.xls]], or for the !ScrumPy VM or linux, [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/Utilities/EnzFitter.ods|EnzFitter.ods]].
  1. [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/Utilities/rmm.gnu|rmm.gnu]] to make a 3D plot of the reversible Micaelis-Menten plot as in the Lecture 2 slides.

 Instructions for use:
  1. Either from a terminal session, change to directory Enzymes and type ''gnuplot'', or , if using Windows gnuplot, open the programme and make Enzymes the working folder. 
  1. To plot an enzyme function, enter a function name with a list of variables and then the equation.  For example:
   {{{
gnuplot> mm(s) = s*V/(Km + s)
gnuplot> V = 100
gnuplot> Km = 2
gnuplot> set xlabel '[S]'
gnuplot> set ylabel 'rate'
gnuplot> plot [s=0:5*Km] mm(s)
gnuplot> Km = 4
gnuplot> replot
gnuplot> 
}}}
  1. ''twoenz.gnu'' generates the reversible Michaelis-Menten graph shown in the Lecture 2 slides.  To plot the graph, open gnuplot and type
   {{{
gnuplot> load 'rmm.gnu' 
}}}
  ''show plot'', ''show fun'' and ''show var'' wil show how the plot has been made.
  1. ''enzfitter.gnu'' determines ''K,,m,,'' and ''V'' for the data in ''enz1.dat''.  
   {{{
gnuplot> load 'enzfitter.gnu' 
}}}
  Use a text editor to see the gnuplot commands ot achieve this.
  1.  ''!EnzFitter.xls'' is an Excel spreadsheet that fits ''K,,m,,'' and ''V''.  It contains the same data as ''enz1.dat''; the initial estimates are in cells B3 and D3.  Go to cell G14 and then select the 'solver' menu item to minimise this cell by altering cells B3 and D3. (This sheet does not work in other spreadsheet software as they don't have the solver add-in: !EnzFitter.ods will open in the !ScrumPy VM, and will allow you to manually adjust the fit.)