Brian Sykes Lab

Version: 5.0.3 - Jun 2012
Download and Installation

Purpose: A graphical X-windows program for binding curve studies and NMR spectroscopic analysis.

Table of Contents

  1. Latest News
  2. Overview and References
  3. Download and Installation

  4. Basic Use and Tutorial
  5. Fitting Functions
  6. Input Files
  7. Output Files

  8. Multiple plots
  9. Data Overlays
  10. Data Exclusion
  11. Parameter Grid Fitting

  12. Settings and Preferences
  13. Customizing your Plots
  14. Appendix: History of xcrvfit

Overview and References

Download and Installation

  1. This software is a self contained tcl/tk starkit which should make installation fairly trivial. See the Release notes for the latest updates. Download the software appropriate for your machine:

  2. Macosx - Double click the download file. You should now get a new file on the desktop (or your download directory) represented by the xcrvfit graph icon. You may want to drag the xcrvfit icon into a more permanent directory like /Applications or keep it on your desktop. Double click on the icon to run the program.

    Linux - Same as the macosx procedure but you may have to explicitly drag the directory from the opened window to the desktop. If you do not get an xcrvfit folder, then un-tar the download file (eg, tar xvf xcrvfit*.tar) and move it to your Desktop.

  3. See install.notes for other ways to install the software and other technical notes.

Basic Usage and Examples for New Users

  1. (Optional) Download our examples It is very helpful to see how xcrvfit works with various examples before trying it out on your own data. For examples, please download our data and examples (2.7MB) file and double click (or un-tar) this file to create the xcrvfit-5.0-x-examples folder. You can run an example by double clicking on the xcrvfit.command file packaged within each example directory. Note: For linux, you may get a dialog asking what to do next, just click on the "Run" button.

  2. Create a directory and place your datafile in it.

  3. Start the program.

    Double click the xcrvfit icon or see these notes for command line usage. If you do not get a graphical window, re-visit the installation section of this manual.

  4. Enter your datafile.

    Use the entry box provided or use the "Browse" button to find it on your file system. Here is example data that you can use. For an explanation of the various data formats that xcrvfit recognizes see the Input Files section. Use the view button to verify your input data file.

  5. Select the fitting function.

    Click and hold the button currently labelled "Line" and select from our current collection of functions. For a more detailed explanation of these functions see Fitting Functions . Once the function has been selected, the program displays the appropriate parameter fields.

  6. Enter each starting parameter value in the box provided and then press the "Show Fit" button.

    A graph of the fitting function is displayed along with a root mean square error value. If you do not see the fitting function, it could be that your starting parameters are not very close.

  7. Press the "Best Fit" button to calculate the best fit of your function to the data.

    Some functions will converge to the best fit function regardless of the starting parameters. Others are very sensitive and a close approximation is required first. If you have difficulties getting convergence try holding one of more parameters as a constant.

  8. Click the Results button.

    Here you can see how every datapoint corresponds to the fitting function. Also, you can see how sensitive each fitting parameter is by looking at the StdDev field.

Fitting Functions

Input Files

Output Files

Settings and Preferences

Customizing Your Plots

Multiple Plots

Data Overlays

Data Exclusion

Parameter Grid Fitting

Appendix: History of xcrvfit

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Questions to: bionmrwebmaster@biochem.ualberta.ca