DEERconstruct

Version 2.2 (702 KB) by Thomas Casey
For testing suppressions in P(r) for Double Electron-Electron Resonance (DEER) spectroscopy data
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Updated 13 Mar 2020

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This App allows users to test the hypothesis that certain components of distance profiles obtained from fitting time domain Double Electron-Electron Resonance (DEER) data are insignificant and can be removed from consideration when deriving a physical meaning from the distance profile.

DEERconstruct accepts the output of DeerAnalysis or .dat files structured as follows:

(:,1) = distance axis
(:,2) = P(r)
(:,3) = time axis
(:,4) = zero time and background corrected time domain data
(:,5) = time domain fit corresponding to P(r)

The time domain signals are computed from each suppression combination using the typical dipolar kernel 'K(r,t)' and compared to the incoming P(r) by calculation of RMSD between their time domain representations.

Cite As

Casey, Thomas M., and Gail E. Fanucci. “Spin Labeling and Double Electron-Electron Resonance (DEER) to Deconstruct Conformational Ensembles of HIV Protease.” Methods in Enzymology, Elsevier, 2015, pp. 153–87, doi:10.1016/bs.mie.2015.07.019.

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MATLAB Release Compatibility
Created with R2019b
Compatible with any release
Platform Compatibility
Windows macOS Linux

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Version Published Release Notes
2.2

-Minor layout adjustments
2.1

-Added option to revert an optimization if the results are illogical
-Added back option to load the DeerAnalysis output. Select any of the _distr, _fit, etc.
2.0

-Transitioned to App Designer
-Dramatically simplified interface and procedure
-Removed all statistical inference, the RMSDs are given for each suppression combination
-Input is now generic
1.3

- Pulled sub-functions out as separate m files
- Use trapz functions instead of sum to get areas of populations
- Updated my email address in the manual
1.2.1.0

-Minor bug fixes
1.2.0.0

-Saving now includes more of the original data and gives the option to save
only the reports for qualified suppressions.
-The distance profiles are now integral area normalized instead of amplitude normalized.
-Updated manual.
1.1.0.0

-Fixed issue where filenames with multiple underscores didn't allow for the correct filename patching necessary for the code to find and load the "_fit" file
-Added calculation of S/N.
1.0.2.0

minor code cleanup, minor bug fixes
1.0.1.0

-Removed {'fontname', 'symbol'} and replaced with call to latex interpreter for users with newer matlab versions
-added zoom and data cursor buttons to the GUI
1.0.0.0