Import data

Instructions

Via the FormatConverter

In Analysis, many different kinds of data can be imported via the FormatConverter popup, which is accessible through M: Other: FormatConverter. To import files, click on the Import menu and choose the file category, the data category and the format of the files to be imported. Based on the chosen file format and data types, popups with different parameters and settings will appear.

Example

We will here as an example illustrate how to import a chemical shift list and a 15N-NOESY-HSQC peak list from a CYANA structure calculation. The used filenames are specific for the project in which the example is based upon.

We start by opening the FormatConverter popup using M: Other: FormatConverter.

Note: In order to read the assignments correctly, we first need to read the chemical shift list that CYANA has used to make atom assignments.

Note: The settings below are project and user dependent and should be adapted based on your own situation.

Importing chemical shifts

First we start with the import of CYANA chemical shifts using: Import: Single files: Chemical shifts: Xeasy from the main menu of the FormatConverter. This raises the xeasy shifts import popup in which we click on the blue arrow to open the additional options menu (note that for Cyana no separate shifts import popup that contains functionality exists):

Here we use the following settings for import:

• • “Chemical shift file to import:”: We click [Select file], and in the file selection popup that is raised we browse and select the import file: filename.prot.

  • “Match existing resonances:”: On.

  • “Link to NMR experiments:”: We select none.

  • “Add to existing shift list:”: None.

  • “Automatically merge shifts:”: Off.

  • “Minimal interaction:”: On.

Note that information that describes each parameter is found by clicking on the [i] button at the right. We click [IMPORT].

• • Now, in the series of popups that are raised, we do as follow:

  • In the Success popup, we click “OK”.

  • In the Run linkResonances popup, we click “Yes”.

  • In the Use fast linking popup, we click “Yes”.

  • In all Select Resonances popups, we select all the resonance choices and click “OK”.

Importing peak lists

Now that we have the correct information loaded for interpreting NOE peak lists, we can import the peak lists using M: Import: Single files: Peaks: Xeasy. This raises the xeasy peaks import popup:

We go through the following settings for import:

• • “Peak list file to import:”: We click [Select file], in the file selection popup that is raised we browse and select the import file: 15N-NOESY-HSQC-cycle7.peaks.

  • “Read as CYANA format:”: On.

  • “Use existing dataSource:”:15N-NOESY:1:15N-NOESY-HSQC.spc (processed).

  • “Peak list name:”: We choose a name.

  • ʻMinimal interactionʼ: On.

We leave all the other parameters to their default values and click [IMPORT].

In the following DataDimRef selection for PeakDims popup we have to map dimensions of the peak list  with the dimension in the spectrum. The chemical shift ranges normally help you to select the correct dimensions. Here we match the peak dimensions as follows:

• • 0 - Dim1(acqu)

  • 1 - Dim 2 (NOESY dimension)

  • 2 - Dim 3 (15N dimension)

Now we click [OK]. After loading the peaks, on the linkResonances popup we answer “NO”, and we can check the peaks in the spectra immediately. To do this, we can open a HHN window and display the 15N-NOESY-HSQC spectrum with the newly loaded peak list and its assignments.

Importing structures

The import of structures into Analysis is most easily done through the M: Structure: Structures command, which raises the Structure: Structures popup. In the {Ensembles} tab (shown below), click on the [Import] button and select the structure ensemble file in the file selection popup.

Structures can be viewed in the structure viewer by clicking on the [Viewer] button.

About how to analyse structures is found here.