EPR Toolbox on Morgan Bye

EasyRefiner

Wed, 06 Feb 2013 10:44:00 +0000

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.

e2af

Thu, 25 Oct 2012 17:38:00 +0000

E2AF or “EPR 2 ASCII folder” is a folder version of E2A, whereby a folder of Bruker EPR files are converted to ASCII data files (readable by any operating system), by default the conversion is to *.csv files (comma separated values). These file formats are easily editable and can be imported into Microsoft Excel, OpenOffice or Origin.

Syntax

1
2
3
4
5


E2AF
E2AF ('path/to/folder')
E2AF (delimiter)
E2AF ('path/to/file.DTA',delimiter)
E2AF ('path/to/file.DTA',delimiter, extension)

Inputs

input1 - The path to a folder; must be in single quotes (')

Savitzky-Golay - sgol

Wed, 30 May 2012 16:44:00 +0000

The Savitzky-Golay smoothing function essentially applies a local polynominal fitting routine to a series of data points to then find the smoothed data points. This has the benefit that for sharp intense peaks (common to EPR) that the line broadening effects and lessening of peak intensity seen by a local moving window average are not seen.

To perform a Savitzky-Golay smoothing functions requires a polynominal order to be defined as well as the window size (or number of data points to be sampled at any given time). We can also weight the window such that future data points are more/less favourable than past points

cwViewer

Fri, 11 May 2012 15:52:00 +0000

cwViewer is a tool for the easy opening, analysis, manipulation and plotting of cw EPR data and superceeds the previous function cwPlotter

With an intuitive user interface, users can quickly create professional looking figures in seconds and export them however they like. Here’s a quick demo introducing the basic features:

cwPlotter comes as part of the EPRtoolbox or as a direct download

Users can quickly load

a single file
a folder of files
a single file with a third dimension (such as power) (*.YGF file)

Manipulate the data using

DEERextract - get data from DeerAnalysis

Fri, 02 Mar 2012 15:00:00 +0000

DeerAnalysis is a program from the team at ETH Zurich that allows for the easy conversion of DEER / PELDOR data into distance distributions. The program itself runs within MATLAB which is renowned for being difficult to make high quality figures with, and DeerAnalysis provides no easy way to obtain the raw data behind the plots that it presents, something that is required if you want to go on to analyse the data.

EPR Converter (e2a)

Wed, 08 Feb 2012 17:57:00 +0000

The Bruker spectrometers output data by default in the Bruker BES3T format, which whilst being perfectly usable is not recognisable by most operating as standard.

This script was originally written for the benefit of the project students in the lab who wanted to plot their cw EPR data in Excel without going to the trouble of learning how to use MATLAB. Or for going back to the spectrometer and trying to export their data in ASCII format.

BrukerWrite - Write Bruker BES3T files

Wed, 25 Jan 2012 15:57:00 +0000

This script allows for the writing of cw-EPR Bruker BES3T files (.DTA/.DSC) files from MATLAB onto your computer

The script uses a graphical user interface to select file name and location, so minimal user line experience is required.

Syntax

1

BRUKERWRITE(x,y)

Write arrays x and y out

1

BRUKERWRITE(x,y,'40uM_MTSL')

A third string argument can be used to name the spectrum, in this case the spectrum will have the title “40uM_MTSL”

addnoise

Wed, 25 Jan 2012 15:46:00 +0000

This script allows the user to add noise to a spectrum, in a manner almost exactly opposite to smoothing data. The script random adds noise to each data point of a spectrum within the range of +/- a percentage of the highest to lowest point.

By default the script uses a value of 5%, so each data point will be randomized to a position + or - 5% of it’s original value (relative to the largest peak). However any value can be selected.

Fsc2Read

Wed, 25 Jan 2012 15:39:00 +0000

This script allows for the loading of cw-EPR Fsc2 files from Jens Törring’s (FU Berlin) program Fsc2 into the MATLAB environment for data analysis.

Syntax

1

FSC2READ

When no inputs are selected a “point and click” interface guides the user through selecting a file

1

FSC2READ ('/path/to/file')

With an input the script opens the selected file

1

FSC2READ ('/path/to/file','plot')

With the second input argument as ‘plot’ the imported file is displayed automatically as a new figure

JeolRead - load Jeol ESR files

Wed, 25 Jan 2012 15:33:00 +0000

This script allows for the loading of cw-EPR Jeol files (*.esr) into the MATLAB environment for data analysis.

Syntax

1

JEOLREAD

When no inputs are selected a “point and click” interface guides the user through selecting a file

1

JEOLREAD ('/path/to/file')

With an input the script opens the selected file

1

JEOLREAD ('/path/to/file','plot')

With the second input argument as ‘plot’ the imported file is displayed automatically as a new figure

R1A to CYM

Tue, 17 Jan 2012 17:12:00 +0000

Traditionally the MTSL spin label bound to a Cysteine residue (Cys) is given the residue code R1A, at least in crystallography structures.

However, some computer modelling programs prefer the identifier CYM. To switch between the two I’ve created this MATLAB script.

Using a GUI interface the user can use a local PDB or download straight from pdb.org and decide to swap from R1A to CYM or CYM to R1A.

If neither a R1A residue or CYM is found then the user is messaged.

Power Saturation Curves

Tue, 17 Jan 2012 17:03:00 +0000

Feature implemented in EPRtoolbox or download now*

Power saturation overview

Determination of the effect of increasing microwave powers on the saturation behaviour of a sample can give information regarding the relaxation properties of the sample. At low powers the amount of signal is linearly proportional to the microwave power. However, at high powers the signal dies away as a function of the inverse square root. Essentially you are saturating the sample, by giving it too much power the spin states cannot relax in the measurable time frame.

PDB Splitter

Tue, 17 Jan 2012 17:00:00 +0000

Feature implemented in EPRtoolbox or download now PDBs are great, however from time to time you only actually want one protein chain to analyse at a time. What you need to do then is split the PDB of many chains into separate PDB files.

This MATLAB script does exactly that. Using local .pdb files (selectable via an open window) or files directly from rcsb.org (using PDB identifier code) up to 4 chains (in this current version) are exported to the current work folder. Important note: This script does use pdbread and pdbwrite from the Mathworks Bioinformatics Toolbox. This is not the ideal open source script I wish it could be, but this is largely due to the widely varying PDB format. I intend to look over how Jescke and Polyhach solve this problem in MMM and perhaps update this script at a later date.

MMM Plotter - 2 spin labels

Tue, 17 Jan 2012 16:56:00 +0000

Feature implemented in EPRtoolbox or download now

MMM is a program from the team at ETH Zurich which allows for the attachment of spin labels in silico. Once attached PELDOR (aka DEER) spectra can be simulate.

With time a temperature assay can be conducted and the distance between spin labels can be monitored.

This MATLAB script combines multiple experiments and plots them into one figure.

Important notes:

In the DEER window of MMM, the figure must be detached and saved to a folder as a .fig file.
All .fig ’s need to be saved to the same folder
The annotations work off of the file names, save your figures as temperatures ie. 298K.fig
The plots will be plotted in folder order, so to get 4K plotted first (ie at the bottom) you need to name your file 004K and adjust it later in Figure Editor

This page previously appeared on morganbye.net[^1][^2][^3]

MMM Plotter - 3 spin labels

Tue, 17 Jan 2012 16:54:00 +0000

Feature implemented in EPRtoolbox or download now

Carrying on from the 2 spin label temperature assay figure creation script. I found myself trying to repeat my success on a system with 3 spin labels.

Such systems give added complication as we now have 3 peaks on the DEER analysis relating to 3 distances. However, in my case I had 2 peaks at very similar distances which ran into each other but I wanted to maintain the underlying peaks as well as the overall trace.

Version History

Wed, 19 Oct 2011 13:26:00 +0000

Release dates:

Version	Release date	Notes
v14.09	7th September 2014	1500+ downloads
v14.05	15th April 2014
v14.02	15th March 2014
v13.12	11th December 2013	NEW: PulseGen
v13.10	24th October 2013	1200 downloads
v13.09	N/A
v13.07	7th July 2013
v13.05	4th May 2013	150000+ lines of code
v13.04	5th April 2013	800 downloads
v13.03	10th March 2013
v13.02	6th February 2013
v13.01	14th January 2013	600 downloads
v12.12	7th December 2012
v12.10	25th October 2012
v12.9	N/A	Youtube demo videos
v12.8	15th August 2012	500 downloads
v12.7	9th July 2012
v12.6	30th May 2012
v12.5	10th May 2012	400 downloads - NEW: cwViewer
v12.2	2nd March 2012	350 downloads
v12.1	25th January 2012
v11.11	19th October 2011	NEW: PowerSat GUI
v11.8	22nd July 2011	NEW: cwPlotter
v11.6	27th May 2011	NEW: PowerSat CLI
v11.5	19th May 2011
v11.4	15th April 2011
v11.3	18th March 2011	First public release

Release information

v14.09

NEW FEATURE: DAPlotter

Takes a saved DeerAnalysis file and plots it rapidly in a graphically pleasing way for notebooks. Figure 1, raw DEER data. Figure 2, raw data after background subtraction with fit. Figure 3, distance distribution

Plotting cw spectra with a g-value x-axis

Wed, 07 Sep 2011 15:10:00 +0000

cw-EPR spectra are common place in the lab, but often we report them simple as intensity against magnetic field in Gauss (G) or milli-Tesla (mT). However, in reality what we are actually interested is the frequency independent g-value.

The problem is that the g-factor by definition is a reciprocal scale (ie non linear, non logarithmic, and reverse scale), which causes a nightmare when trying to plot in MATLAB.

For this reason I have created two similar scripts. The first plotgx creates a new figure (such as that shown above)

cwPlotter - the cw EPR plotting tool

Fri, 22 Jul 2011 15:18:00 +0000

This script has been superceded by cwViewer

cwPlotter is a tool for the easy opening, analysis, manipulation and plotting of cw EPR data.

With an intuitive user interface, users can quickly create professional looking figures in seconds.

cwPlotter comes as part of the EPRtoolbox or as a direct download Users can load

a single file
a folder of files
a single file with a third dimension (such as power) (*.YGF file)

They can then manipulate the data using

Amino Acid Converter - AAconverter

Wed, 15 Jun 2011 13:54:00 +0000

The amino acid converter (AAconverter) is a small user interface that I’ve put together for MATLAB that will transform amino acids between the 1 letter or 3 letter representation. Useful for any amount of DNA work.

Simply, type or paste (from the clipboard) in one of the boxes and then press the appropriate arrow. The program will then convert between amino acid codes and then format the original and new sequence into easy to view formats (1 letters into groups of 10, 3 letter into groups of 5).

BrukerRead - load Bruker BES3T EPR files

Thu, 19 May 2011 13:09:00 +0000

This script loads Bruker EPR files into MATLAB.

The script has been extensively tested with Bruker BES3T files (.DTA/.DSC). Originally it was built for cw-EPR files, but functionality has been added for 3 dimensional cw experiments (.DTA/.DSC/.YGF) and for pulsed experiments such as field swept echoes (FSEs) and Fourier induced decays (FIDs). Functionality for advanced and 3D pulsed experiments such as HYSCORE, ESEEM, ENDOR and PELDOR is more supported.

BrukerRead also supports the older Bruker file format (.spc / .par) still used by the Bruker EMX instruments.

cwplot

Thu, 19 May 2011 12:58:00 +0000

Implemented in the EPRtoolbox or direct download

This script is a quick way of presenting cw-EPR spectra by taking data from arrays of magnetic field and intensity

1

cwplot(x,y)

Where, x and y can have any number of columns (so long there is the same number). With optional input arguments we can specify the separation between spectra and even offset.

1

cwplot(x,y,sep,offset)

This page previously appeared on morganbye.net[^1][^2][^3]

Peakfinder

Wed, 27 Apr 2011 10:29:00 +0000

Feature implemented in EPRtoolbox or download now (requires fpeak)

A simple MATLAB script to open an EPR spectra (requires eprload from S. Stoll’s EasySpin), baseline corrects to zero, plots the result and then finds all of the peaks.

It features a GUI to select the file in question, and the option of automatic settings or manual settings as well as a noise filter for small variations about 0. Output to the Command Window lists the exact positions of the peaks, first column is magnetic field, second the intensity.

MMM individual rotamer PDBs

Wed, 27 Apr 2011 10:27:00 +0000

This feature has been removed from the EPR toolbox as of version 12.9, due to MMM 2011.2 directly implementing this feature. This page remains for information purposes only. Feature implemented in EPRtoolbox

MMM by default saves calculated rotamers as a rotamer library PDB. This when viewed within PyMOL causes a bit of a problem as you’ve now lost the protein to which the rotamers are supposed to be attached.

Using scripts not distributed with MMM provided by Yevhen Polyhach and Gunnar Jescke, you can make instead make MMM output each rotamer as an individual PDB with the spin label attached to the protein.

cw Normaliser (cwnorm)

Wed, 27 Apr 2011 09:45:00 +0000

Feature implemented in EPRtoolbox or download now

cw-EPR are useful, but when comparing numerous spectra things can become quite challenging especially when different powers or sample concentrations are used.

By normalising (normalizing by American spelling) spectra, key features instantly become more comparible.

This MATLAB function acts discretely to normalise a cw-EPR spectrum or can be used within a script to act upon many spectra.

Usage:

1

y = cwnorm(y)

Normalises matrix y (ie the y axis) between -1 and 1.