Raven: Rapid Auto-determination of Variables Encoded by NMR
With the advance and complexity of NMR experiments, analysis of large amounts of data benefit from automation. Recently, in particular with the advent of fast spinning, measurement of protein dynamics in the solid-state became more practical and more accurate. In particular, many proteins and molecular assemblies with known structures (from either X-ray crystallography, cryoEM or NMR) can be readily prepared and analyzed for their dynamic properties. Such experiments are mostly performed as pseudo-3D, where two dimensions account for the isotropic shifts of two spins in order to provide spectral resolution and correlations, and a third dimension accounts for the modulation of some NMR parameter that is related to dynamics.Examples are the measurement of dipolar order parameters, CSA values, pH, relaxation and more. Since the parameter reporting on dynamics is modulated for each cross-peak, many such curves are generated by the experiment and require the correct assignment of the corresponding crosspeaks.Automation of this process has the benefit of reducing errors, identifying and sorting ambiguous and non-ambiguous signals, and speeding up analysis by generating and fitting all curves simultaneously.
The software 'Raven' is designed to provide simple and quick automated cross-peak assignments of 2D and 3D spectra when an assignment table exists (and potentially a tertiary or quaternary structure), and given sets of spectra that exhibit intensity variations, provide automated intensity curves for each assigned cross-peak.Those curves can then be analyzed using proper theoretical approaches or fit to some pre-calculated energy landscapes.
Latest News:
* 24.12.2017: The negative intensities are now displayed correctly in the0 Cross peaks Analysis tool.
* 19.3.2018:
1. Calibration histograms were fixed.
2. The database of chemical shifts was updated according to the bmrb website.
3. The structural coordinates are now loaded correctly when the loaded assignment table is incomplete.
Setup:
Download from Zenodo database: Raven Version 2.0 28-8-2018.rar
Tutorial: Raven Tutorial Version 2.0 28-8-2018
Requirements: Windows 7/8/10.
Run the setup file "Setup.exe" and follow the instructions.
Note: Installation in the \program files\ folder is not recommended. This folder is somewhat protected by the system, hence, output files that were saved in this folder will not work properly. In case Raven was installed in this folder or other protected folder, one of the following approaches could be used:
1. Reinstall Raven in another folder.
2. Run Raven as administrator (by right-clicking the shortcut icon).
3. Make sure to save your results in another folder, which is not protected by the system, for instance: "C:\Raven\Protein Results\".
In case the installation failed, or do not progress for a very long time:
1. Run the setup file as administrator and reinstall Raven in another folder which is not protected by the system, for instance D:\Raven\.
2. Delete the temp files on Windows directory:
2.1 Press Windows Key + R (or start and search for %temp% directory) and enter %temp%.
2.2 Delete all files from the %temp% directory.
2.3 Reinstall Raven.
In case you are not able to install or update Raven, try to uninstall "National instruments Software" and reinstall Raven.
In case you still experience problems, please contact us at tomaharoni88 AT gmail.com or amirgo AT tauex.tau.ac.il.
You can run Raven by using the shortcut created on your desktop.
Citing Raven:
If you publish a work that use Raven, please cite the following article:
T. Aharoni, A. Goldbourt, Rapid automated determination of chemical shift anisotropy values in the carbonyl and carboxyl groups of y21m-fd bacteriophage using solid state NMR, J. Biomol. NMR. (2018) 113. doi:10.1007/s10858-018-0206-1.