Using the GUI

How to start the User Graphics Interface (GUI)

You may use ARIAs graphical user interface (GUI), an XML-editor or a text-editor to display and edit your project. However, ARIA's GUI is intended to streamline the project-setup and further provides brief descriptions / help for most of the parameter settings. For starting the GUI with the project "new_project.xml" use the command:

aria2 --gui new_project.xml

or

aria2 -g new_project.xml

If the project file is omitted, the GUI starts without loading any project.

Project

• Creating a new ARIA project

Project > New

• Adding Spectra
  

Add > Spectrum

• Fixing iteration related parameters
  

Protocol > Iterations > 0

• Molecular dynamics parameters
  

Structure Generation > CNS > Dynamics

Adding CCPN Data

• Setting CCPN Project
  

Project > CCPN Data Model, click Browse Button, select CCPN project

• Getting Molecular System from CCPN Project

Project > Molecular System, choose "CCPN" format, click select.
Select Molecular System, click OK. If more than one chain is present, select chain(s)

CCPN Name now contains the name of the Molecular System followed by the chains codes.

• Adding Spectrum from CCPN Project

Add > Spectrum
Project > Data > Spectrum > #1
Select the chemical shift list by selecting "CCPN" format in the "Chemical Shift List" Frame.
Then click on Select. Choose Shift List.

Now select "CCPN" format in the "Spectrum" frame.
Click Select and choose the corresponding Spectrum.

• Adding Unambiguous Distance Restraints from CCPN Project

Add > Unambiguous distances
Project > Data > Unambiguous Distances > #1
Select "CCPN" format and click Select.

Choose the Constraint List.

Options:
Filter contributions: The restraints will enter the ARIA violation analysis machinery to filter restraints according to the violation analysis in order to reduce ambiguity

Calibration: Determine how the restraints should be calibrate by ARIA.
All iterations : the restraints will be calibrated at each iteration.
Not 1st Iteration: the restraints will not be calibrated at all iteration except the first one.
Disable: the restraints will never be calibrated by ARIA.