ER-07-Final
Wednesday, 6th February 2013

EasyRefiner

Faced with fitting well over 30 experiments at room and low temperature at multiple frequencies, as all of my experiments are spin-labelled mutants of the same protein then surely their EPR properties would be similar. I decided that there must be a better way of using EasySpin than manually inputting each file in time and time again.

What if I could queue an entire folder of files, set up some rough parameters and then get EasySpin to do the hard work? Why not use a rough EasySpin search for parameters and then input the rough parameters back into EasySpin with finer searches and refine the numbers? By queuing a folder of files I could set up my PC at the end of the day to run overnight and come in in the morning and be greeted with fitted spectra.

And so, was created EasyRefiner (available as part of the EPR toolbox)

EasyRefiner

EasyRefiner is called from MATLAB with the command “EasyRefiner” which calls a GUI

By clicking, on “Load file” of “Load folder” brings up a standard file or folder selection window. As normal for the EPR toolbox, this has been designed for Bruker files, support may be added at some point for Jeol/Varian as and when I get some files to play with.

Once a file/folder is selected the file/s are processed and added, with their titles being listed in the Files box.

Next you need to set up some standard EasySpin parameters. For ease of use I’ve included some defaults:

Select one from the list and click load – more can easily be added in the source code or email me and I can add them.

Rounds of fitting can be turned on or off using the check boxes for the rounds. When happy with the variables check the Options.

Experiment settings

Experimental settings for microwave frequency and magnetic field do not need to be inserted as these are automatically pulled from the data files. This is done for ease and because a series of queued files will have slightly differenct settings.

If you want to add your own other settings ensure you use “Exp.{variable} = {some value};”

Option settings

Output location

The output location by default is whatever the MATLAB Current Folder was when EasyRefiner was called. You can change it by clicking Change. This will start a GUI and allow you to select a folder.

Saving figures

This option will automatically save all figures from EasySpin as they are created. They are saved as MATLAB .fig files in the output folder with round 1 being saved as {file title}r1.fig, round 2 as {file title}r2.fig and round 3 as {file title}r3.fig

Keep figures open

This option ensures that all figures are kept open, otherwise they are automatically closed after they have been saved.

Save log file

Saves a log text file of the fitting run to the output location. Basically this is a read out of all the information presented in the information box

Delay

If running a long queue, you may want to protect your CPU from overheating. To avoid this a delay can be introduced between fits to allow heat to dissipate. By default this is set at 5 seconds, but will obviously increase the time of any run.

Fitting methods

You can select the fitting method that EasySpin uses using the list boxes. EasySpin fitting using garlic, chili and pepper are allowed and spectra can be fitting using any of the EasySpin methods such as simplex, Monte Carlo, genetic, grid, etc

Options

Should any options not be covered otherwise that you wish to include, include them in the text box in the standard fashion “Opt.{variable} = {value}”

RUN!

Finally when happy with all settings click RUN!

A progress bar for the queue will pop up, a lot of information will flash through the information box and EasySpin will be called.

Once a fit is made, the parameters fitted from the first round will be piped into the second round as the starting parameters (ie. Exp is updated)

With the “Keep figures open” option, EasySpin figures are then stacked on top of each other

 

About Morgan Bye

Scientist, programmer and all around techie

Category

EPR toolbox