Opening spectra in Sparky

From NMR Wiki

NOTE: Sparky commands shown in bold

Sparky opens three types of files:

• .ucsf - binary raw data files
• .save - plain text files containing information about spectrum display and link to corresponding .ucsf file
• .proj - plain text project files containing links to .save files and more project-specific information

Opening files with menu's

Go to 'File' menu, click 'Open...', select appropriate .ucsf or .save file and click 'Open' button.

If you are starting with .ucsf file (raw data file), then you may need to:

• start sparky
• recommended: change keyboard delay setting to make interaction with software easier
• adjust display aspect ratio (vt)
• adjust contour levels (ct)
• select colors for the spectrum (also in ct)
• when opening 3D and 4D spectra you might need to select which plane is to be displayed

File paths in .save and .proj files

If you have problems opening sparky files on your computer, this section may be able to help.

As metioned above, sparky uses .save and .proj files to store all sorts of "metadata" about the spectra, while .ucsf files are used for the storage of the binary data.

Among other data, .save files contain a path to the corresponding .ucsf file and .proj file contains a list of paths to the relevant .save files.

When transfering sparky projects (a collection of files with above three extensions) between computers or simply moving them from one directory to another paths to the files that are stored in .save and .proj files may break. This issue will unfortunately need a manual intervention, but is quite easy to fix.

Open .save files with your favorite text editor and find a line that looks like this:

pathname ../project-X/tocsy-h2o-25C.ucsf

Delete the relative path part and make the line into

pathname tocsy-h2o-25C.ucsf

Similarly with .proj file (say project-x.proj) - find a section:

<savefiles>
/path/to/project-X/gcosy-d2o-25C.save
/path/to/project-X/noesy-100ms-d2o-25C.save
/path/to/project-X/noesy-100ms-h2o-25C.save
/path/to/project-X/tocsy-d20-25C.save
/path/to/project-X/tocsy-h2o-25C.save
<end savefiles>

and modify it to:

<savefiles>
gcosy-d2o-25C.save
noesy-100ms-d2o-25C.save
noesy-100ms-h2o-25C.save
tocsy-d20-25C.save
tocsy-h2o-25C.save
<end savefiles>

Now the project will be openable with commands

cd /new/dir/for/project-X
sparky project-x.proj

No each time your project will be openable on your computer, however each time you'll need to share the project, the paths will need to be cleaned up again.

Opening files from command line

On Unix systems you can simply type:

sparky somefile.ucsf

or

sparky somefile.save

or

sparky somefile.proj

Then you may have to adjust spectrum display as described in the previous section