Amaterasu¶

This program is intended to simplify the screening, acquisition, processing and model fitting of large on- and off-resonance R1ρ relaxation dispersion NMR datasets in an automated manner for the analysis of chemical exchange phenomena in biomolecules.

The program is described in this publication:

Walinda, E., Morimoto, D., Nishizawa, M., Shirakawa, M., and Sugase K.,
Efficient identification and analysis of chemical exchange in biomolecules by R1ρ relaxation dispersion with Amaterasu.
Bioinformatics, 32, 2539-41 (2016)

http://bioinformatics.oxfordjournals.org/content/32/16/2539

Bug reports, questions or comments should be addressed to: walinda.erik.6e (at) kyoto-u.ac.jp.

Amaterasu (original version)¶

The original version works from 1D NMR spectra. This is nice for small proteins, where resonance overlap is no problem. However, for challenging samples, we recommend the newer version called Amaterasu’kai.

Getting the program to work¶

Amaterasu requires the following packages:

nmrglue

http://www.nmrglue.com

Version 0.6 is required and is included in the package. Thus, installation should not be necessary.

Moreover, nmrglue can be easily installed using:
```
git clone https://github.com/jjhelmus/nmrglue
cd nmrglue
sudo python setup.py install
```
nmrPipe

An installation of nmrPipe is required because the program uses the peakpicker included in nmrPipe to get the intensity of the crosspeaks.

nmrPipe can be downloaded here:

http://spin.niddk.nih.gov/NMRPipe/
GLOVE

This software is required to fit the final R1rho relaxation rates to a theoretical model. GLOVE is freely available from the laboratory of Peter Wright:

http://www.scripps.edu/wright/?page_id=17
numpy and scipy

Numpy and scipy are already installed on many unix systems. If not, they are easily installed by your distribution’s packet manager or via pip:
```
sudo pip install numpy
sudo pip install scipy
```
Alternatively, you may download numpy and scipy from:

http://www.numpy.org

http://www.scipy.org
PyQt

For the GUI of Amaterasu, version 4 or 5 of PyQt is required.

As with numpy and scipy, this package may already be installed on your system. If not, it is easily installed by the respective package manager (port / brew on MacOS, dnf / yum on fedora, apt-get on Ubuntu/Mint, etc.).

Alternatively, you may want to get PyQt directly from the site:

https://www.riverbankcomputing.com/software/pyqt/download
matplotlib

Matplotlib is required to plot the raw data (your NMR spectra) to verify that the raw data look good and no artifacts were introduced by the automated processing by Amaterasu.

As with the other dependencies, matplotlib is easily installed by a package manager, or downloaded from the website:

http://matplotlib.org

or via pip:
```
sudo pip install matplotlib
```

The Amaterasu package includes the spreadsheet for setup of the relaxation dispersion experiment, Bruker pulse programs and analysis software.

The package can be downloaded here - amaterasu-1.0.tar.gz

Again, it is noted that this is the first version of Amaterasu, which works only with 1D experiments. This is not sufficient in the case of challenging proteins with highly overlapping spectra. For difficult proteins, we recommend to use 2D acquisition and process the data using a different version of Amaterasu (i.e. Amaterasu’kai).

Using Amaterasu (original version)¶

Convert Bruker data to NMRPipe format:
```
./fid.com
```
Split pseudo-2D experiment into 1D parts:
```
./split2D.com
```
Run Amaterasu by executing:
```
./amaterasu
```

For the demo datasets, please execute ./fid_demo.com in the respective demo data folder. Steps (1-2) are combined in the script fid_demo.com.

Amaterasu’kai¶

Just as the original version of Amaterasu, this program helps to process R1ρ relaxation dispersion NMR datas. The difference is that it works from F1F2-selective 2D experiments. The F1F2-selective experiment is described in this publication:

Walinda, E., Morimoto, D., Shirakawa, M., and Sugase K.,
F1F2-selective NMR spectroscopy
J Biomol NMR (2017)

http://link.springer.com/article/10.1007/s10858-017-0113-x

The pulse program is available for download in the pulse program section of this site.

Please feel free to inquire, if you have questions regarding the setup of these experiments.

Pseudo-4D version¶

The latest version works from pseudo-4D experiments. The benefit of using pseudo-4D experiments is that only a single experiment has to be set up to collect relaxation dispersion profiles of any number of resonances.

The current version of Amatarasu’kai package can be downloaded here - amaterasu-kai.zip

Amaterasu’kai requires the following packages:

nmrglue http://www.nmrglue.com

Version 0.6 or higher is strictly required. Older versions will throw an error soon after execution. nmrglue is easy to install:
```
git clone https://github.com/jjhelmus/nmrglue
cd nmrglue
sudo python setup.py install
```
nmrPipe

An installation of nmrPipe is required because the program uses the peakpicker included in nmrPipe to get the intensity of the crosspeaks.

nmrPipe can be downloaded here:

http://spin.niddk.nih.gov/NMRPipe/
GLOVE

This software is required to fit the final R1rho relaxation rates to a theoretical model. GLOVE is freely available from the laboratory of Peter Wright:

http://www.scripps.edu/wright/?page_id=17

Amaterasu’kai Manual¶

Running Amaterasu’kai¶

Amaterasu’kai itself requires no installation. Simply extract the downloaded archive.

The downloaded archive contains two kinds of demo data. One is a screening experiment, in which a weak and a strong spinlock is applied to all resonances seen in a [1H, 15N]-HSQC spectrum. This experiment is used to identify residues that exhibit chemical exchange.

To process these data using Amaterasu’kai, execute:

./amaterasu.py --data=demo_screening -r -s

The above command uses automatic phase correction. If you would like to specify the phase correction explicitly (which sometimes gives better results), run:

./amaterasu.py --data=demo_screening -r -s -m --p0=[phase]

The -r flag tells Amaterasu’kai to actually run. The -s flag tells the programm that this is a screening experiment, as opposed to a full experiment with a large number of spinlock values. The -m says that the phase correction is specified manually and this phase is specified using the –p0 flag. The location of the experimental data is specified with the –data flag. This is the folder containing the experimental data in Bruker format.

So, for example:

./amaterasu.py --data=demo_screening -r -s -m --p0=14

The above command would apply a ph0 phase correction of 14 degrees to all data.

The second type of experiment for which Amaterasu’kai is used is a acquisition of complete relaxation dispersion profiles. Here, the experimental setup differs in that a larger number of spinlock powers is used. To process such a dataset, for example the demo data:

./amaterasu.py --data=demo_full -m -r

Again, to specify the phase correction specifically:

./amaterasu.py --data=demo_full -m --p0=0 -r