In this tutorial, we will execute the ARTINA application, which performs end-to-end automated protein structure determination. ARTINA requires as input only the protein sequence (one letters code) and processed NMR spectra (Sparky, Bruker, XEASY and NMR Pipe formats are supported). Since our example datasets use Sparky data format, it will be used as default in this tutorial.
In the first step, prepare all required input files for ARTINA, such that they are easily accessible later. A local directory listing of example input files is presented in the Figure 1.
Additionally, some spectra have special tags in their filenames (e.g. @ALI, @ARO, @POS). These tags provide additional information about the spectrum. You can find more about their meaning in the NMRtist dictionary. The underlying logic is the same as for spectrum types. If tags are provided in the filenames, they are recognized automatically. Otherwise, this information must be provided manually.
NMRtist projects are means to organize NMR data within the system. Each project is permanently bound with a single fasta sequence, which cannot be changed after the project has been created. It is possible to have several projects with the same sequence (e.g. for datasets recorded under different experimental conditions).
To create a project, use the "New Project" button available in the top menu:
The "New Project" form, filled with exemplary data, is presented in the image below:
Finally, submit the "New project" form by pressing the "Create" button.
At the moment, the newly created project contains no experimental data:
Simply drag all your Sparky spectra, and drop them in the blue upload area to start the data transfer. Do not leave the page while files are being uploaded! You can find information about other supported formats in the NMRtist dictionary.
After the upload is completed, the page should resemble the image below:
Before running any application, you must specify the metadata related to the uploaded files, such as the spectrum types and the axes order. You can do this conveniently using the interface available in the "Project summary" (visit the "Summary" link in the left menu).
The interface displays all files uploaded to the project:
In case you need to provide the metadata for your spectra, the following information is required:
After filling in the missing information, the "Project summary" doesn't report problems anymore
Once spectra are properly added to the project, they can be used as input for NMRtist applications. Available applications are listed on "Applications" page, accessible through the left menu:
To prepare an application call, press "RUN APPLCIATOIN" next to the name of the chosen application:
Subsequently, specify the input data for the application call:
The exemplary application call definition, with all spectra used as input, is shown below:
Once the "SUBMIT JOB" button is pressed, your job will be submitted to the system queue, where it waits for the computational resources. Note that each application call is associated with a certain cost, expressed in CPU and GPU hours, that is used to prioritize application calls. Under heavy load, NMRtist will execute jobs in the order, which is defined by the number of CPU/GPU hours used by a user within the last 30 days.
To track the status of your application calls, visit the "Results" page using the link available in the left menu:
This is the end of the tutorial. If you have managed to submit an application call, it will be processed soon by NMRtist. Once your job status changes to "Finished", you will be able to access its results using the "Open" button.