Experiment : Open Spectra

Locate Spectrum Data for Use in CCPN Project

This popup window enables the user to locate spectrum data within a file system and associate the files (typically binary) with an experiment and spectrum name so that it may be visualised and accessed within the current CCPN project. Spectra of many different origins and file formats may be loaded, which currently includes Bruker, Varian, Felix, NMRPipe, NmrView, SPARKY/UCSF, Azara and the factorised shape format “USF3”. Depending upon the file format of the spectrum, data loaded the user may be required to either select a parameter file which then refers to the actual spectrum intensity data; this is true for Bruker “procs” and AZARA ”.par” files, or alternatively a spectrum data file itself that contains referencing information; this is the case for SPARKY/UCSF, NmrView and NMRPipe spectra.

The layout of the popup involved two sections; the upper of which is for navigating to and selecting the spectrum or parameter files within the file-system, and the lower is for specifying how each spectrum is loaded into the CCPN project. It should be noted that when spectrum parameters are read the first time, the relevant information is copied into the CCPN project, where it may be adjusted independently of the original file information. No copies of the spectrum intensity data are made, the CCPN project merely refers to the spectrum data on disk, although the data file for a loaded spectrum may subsequently be moved or replaced.

In normal operation the user first selects the kind of spectrum file format that will be loaded via the upper “File format” pulldown menu and then checks that the “File type” pulldown (toward the bottom of the file browser) is set to detect the appropriate kinds of filename; if a helpful file name filter is not available the user can add one via the “Manual Select” field, taking care to add any wild-card symbols, like the asterisk in “*.ft3”. Next the spectrum data or parameter files, appropriate to the selected format, are located by navigating within the file-system browser. When the required spectrum files are visible the user selects one or more to load. Multiple file selections may be made using left-click with <Ctrl> (toggle selection) or <Shift> (select range). It should be noted that when selecting Bruker files, when using the standard Bruker directory structure, the user only needs to navigate to the numbered spectrum directory; by default the “procs” file two levels down is searched for, e.g. “123/pdata/1/procs” is shown in the directory containing the “123” directory.

When spectrum or parameter files are selected in the file table, the lower “Spectra To Open” table is filled to reflect the selection. The user should then be mindful of the settings within this table and may choose to edit various things by double-clicking on the appropriate cell. Typically the user just adjusts the name of the independent “Experiment” and “Spectrum” records. These names are usually concatenated like “expName:specName” in CCPN graphical displays so there is no need to repeat a name in both fields; this only takes up more space. The Experiment, which is a record of what was done experimentally, commonly has a short name like “HNCA” or “HSQC_298K” so the user readily knows how to interpret the experimental data. The Spectrum, which is a record of the data that was collected, commonly has a short name to identify the spectrum number or file name. An Experiment record may contain several Spectrum records, so the spectrum’s name need minimally only identify it amongst others from the same experiment. The Shift List value may be changed if the user knows that the experiment represents a distinct set of conditions, with different spectrum peak/resonance positions, to existing or other experiments being entered. Each shift list will be curated separately, to give separate chemical shift values for assignments made under different conditions (even when relating to the same atoms). The shift list that an experiment uses may also be changed at any time after loading.

When all spectra and options are specified the [Open Spectrum] button will load the relevant data into the CCPN project. If the “Skip verification dialogs” option is set it is assumed that all of the spectrum point to frequency referencing information, and any data file references, are correct. Otherwise, the user will be prompted to confirm the file details and referencing information for each spectrum in turn. Finally, after loading the user is asked to set the type of NMR experiment, in terms of general magnetisation transfer pathway, that was performed.

Caveats & Tips

If the name of an Experiment that is already within the CCPN project is used, then the loaded spectrum will (assuming it is compatible) be entered under that existing experiment record; no new experiment entity will be defined. The user may legitimately use this feature to load several spectra that relate to the same experiment; typically where spectra are different projections. To facilitate this the “Use shared experiment” option can be selected.

Although experiments and spectra may be renamed after loading, a spectrum record may not be placed under a different experiment once created; deletion and re-loading is the only mans of achieving this, and care must be taken in transferring any assignments.

Main Panel

File Selection

pulldown File format: Selects which kind of spectrum file is being loaded; what its data matrix format is

Table 1
Name Name of file, directory or link
Size Size of file in bytes
Date Date of last modification

button Back: Go to previous location in history

button Forward: Go forward in location history

button Up: Go up one directory level

button Top: Go to root directory

button Home: Go to home directory

button New: Make a new directory

button Refresh: Refresh directory listing

pulldown File type: Restrict listed files to selected suffix

check Show hidden: Show hidden files beginning with ”.” etc.

pulldown Dir path: Directory navigation to current location

Spectra To Open

check Skip verification dialogs: Whether to allow the user to check file interpretation and referencing information before the spectrum is loaded

check Use shared experiment: When selecting multiple spectrum files, whether the loaded spectra will all belong to (derive from) the same experiment; useful for projection spectra etc.

Table 2
Experiment A short textual name for the experiment record that the loaded spectrum will belong to; may be a new experiment or the name of an existing one (Editable)
Spectrum A short textual name to identify the spectrum within its experiment; typically a few characters or spectrum number, rather than a repeat of the experiment name (Editable)
File The location of the file, relative to the current directory, that the spectrum data will be loaded from
Windows Sets which window or windows the spectrum will initially appear within once loaded (Editable)
Shift List Sets which shift list the experiment (and hence loaded spectrum) will use to curate chemical shift information; can be changed after load time (Editable)

button Open Spectrum: Load spectrum or spectra into the CCPN project using the selected file(s)

button Help: Show popup help document

button Close: Close popup

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