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
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 |
Back: Go to previous location in history
Forward: Go forward in location history
Up: Go up one directory level
Top: Go to root directory
Home: Go to home directory
New: Make a new directory
Refresh: Refresh directory listing
File type: Restrict listed files to selected suffix
Show hidden: Show hidden files beginning with ”.” etc.
Dir path: Directory navigation to current location
Spectra To Open
Skip verification dialogs: Whether to allow the user to check file interpretation and referencing information before the spectrum is loaded
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) |
Open Spectrum: Load spectrum or spectra into the CCPN project using the selected file(s)
Help: Show popup help document
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