Experiments: Open Spectra

This popup window is used to select various parameter and data files for NMR spectra. When a spectrum file is opened a spectrum object is created in the current project. These spectra may be associated with new or existing NMR experiments.

Skip verification dialogs

When you open a spectrum or spectra you are asked to verify crucial data like the isotope types, the number of points, the referencing information, etc.  If you are absolutely sure that Analysis will open your file correctly then you can skip the verification dialogs.  Note that no matter what, you are asked to specify the Experiment Type, e.g. HSQC, in the {Specify Experiment Types} tab of Experiments: Edit Experiments.

File format

Allows the user to specify the format type of the selected spectrum / parameter files. Available options are:

• • Azara

  • Bruker

  • Felix

  • NMRPipe

  • NMRView

  • UCSF

  • Varian

  • Factorised

File selection

This section of the popup allows the user to navigate file systems and open a directory from which multiple selected spectra can be selected for loading. The type of files that are selected in the table depends on the type of selected file format. For example, to load spectra that have been processed with Azara, the parameter files are selected. Whereas for Felix data the spectrum data files, which contain header information, themselves are selected. The selected files specify how spectral data should be interpreted and what the location of the data is.

Name

The name of the data or parameter file.

Size

The size of the file on disk.

Date

Last modification date/time of the file or directory.

Back

The Experiments: Open Spectra popup

Go back. Navigates back to a previous location.

Up

Go up one directory.

Forward

Go forward. Navigates forward to a previous location.

Top

Go to top directory.

Home

Go to the home directory.

New

Create a new directory through the New directory popup.

Refresh

Refresh. Refreshes the directory listing. Useful after changes have been made to the directory contents whilst the popup was open.

File name

This text input area shows the currently selected file.

Directory

This text input area shows the current directory with its full path. Can be used to quickly navigate to directories higher up in the directory tree.

File type

A filter to limit the files being shown, specific to each file format.

Show hidden

This checkbox toggles the display of hidden files on or off. Hidden files are typically files starting with a dot, e.g. '.cshrc'.

Dir path

This pulldown shows the current directory and its parent directory tree. Can be used to quickly navigate to directories higher up in the directory tree.

Spectra to open

This table lists the spectra that can be created from the selected data and parameter files. Each selected file gives rise to a spectrum for a specified experiment.

Experiment

The name of the experiment into which spectrum is stored. Analysis provides a default name, e.g. Expt_1, but it is recommended to change the name such that it describes the experiment.

Spectrum

The name of spectrum. Analysis provides a name based on the file name, but which can be changed by the user. Combined with the experiment name, this is how Analysis labels the spectrum in its dialogs, etc.

File

The actual name of the data file or header file that points to the data file.

Windows

The windows that the spectrum will be displayed in, amongst the windows that are compatible with it. The possibilities are

• • None

  • First

  • All

A compatible window will be created if none exist.

Shift List

The Chemical Shift List that contains the shifts for this experiment. Note that chemical shifts are calculated by averaging over assigned peaks in the experiments that share a shift list. Experiments done at different temperatures, different PH, etc. should normally use different shift lists.

Open spectra

Opens the selected spectra with specified settings. Depending on the settings, the user will be guided through the popups to provide additional information of the import of the spectra into the project:

• Verify Spectra

• Experiments: Edit Experiments