POKY User Manual

Common Commands

Sparky offers a variety of two-letter accelerators to streamline your workflow. Below, you’ll find a categorized list of these commands along with brief descriptions of their functionalities.

• cf opens the command finder window

File IO

• fo to open a spectrum or a Sparky / POKY save file
• jo to open a Sparky / POKY project
• fs to create a Sparky .save file (a config file with various display settings)
• js to save the project (also a config file for window layout etc.)

Spectra display and looks

• xa: Show nucleus type on axis.
• xe: Special Python command for saving the peak list in Xeasy format.
• xr: Roll axes. Useful for navigating 3D and 4D spectra.
• xx: Axis transpose. Swaps the axes.
• yt: Synchronize axes of various spectra. Ideal for peak picking in 3D and 4D spectra using a 2D as a reference.
• zf, zi, zo, zp: Zoom full spectrum, zoom in, zoom out, and zoom to the previous view, respectively.
• ec: Easy contour dialog allowing you to adjust all loaded spectra. RECOMMENDED
• ct: Adjust contour levels and colors. Better use ec.
• cl: Adjust the color of an ornament.
• oz: Adjust the size of an ornament.
• ol: Overlays spectra.
• ci: “Inverse background color”: in fact, this dialogue allows changing the color of the selected peak (POKY build 29. Aug 2024)
• vt: View settings. Adjusts various spectral settings, including aspect ratio of axes (e.g. expand one axis by increasing Aspect).

Peak and Spectrum Manipulation

• a1, a2, a3: Add spectral width (SW) to a peak in the F1, F2, or F3 dimension. Useful for aliased spectra.

  NOTE: sweepwidth is an term incorectly used to refer to spectral width.

• A1, A2, A3: Subtract SW from a peak in the F1, F2, or F3 dimension. For handling aliased spectra.
• at: Assignment tool. Assists in assigning peaks.
• dr: Delete resonances not used in any peak assignment. Cleans up the resonance list.
• eu: Undo the last peak manipulation.
• it: Integration tool for peak integration.
• kr: Restrictive peak picking tool. Allows using one peak list as a guidance for peak picking in another spectrum. E.g. 1H-15N HSQC -> 4D HCNH NOESY.
• lt: Opens the peak list for a given spectrum, offering various options.
• oc: Ornament copy. Copies assignment/label information between spectra.
• op: Ornament paste.
• pa: Select all peaks in a spectrum.
• pc: Peak center. Refines the centering of peaks.
• pv: Provides a list of sizes and peak counts in all open spectra.
• rl: Opens the resonance list for the project, offering various functions and displays.
• rp: Read in a list of peaks in Sparky format from external tools like AutoAssign or PINE, aka load sparky list file with assignments to existing spectrum:

    Assignment         w1         w2  
      Q47NE2-HE22    110.585      6.621 
      Q77NE2-HE22    111.920      6.782 
      N29ND2-HD22    111.860      6.792 
      N73ND2-HD22    111.747      6.806 
      N39ND2-HD22    111.951      6.842 
      N85ND2-HD22    111.527      6.876 
      N64ND2-HD22    114.934      6.913 
           G50N-H    106.253      7.121 
      Q47NE2-HE21    110.576      7.267 
            85N-H    110.658      7.322 
  

Note: For peaks with assignments not following the convention [A-Z][0-9]+[A-Z0-9’]+-[A-Z0-9’], use a custom script that modifies the .save file to ensure compatibility.

• rr: Resonance rename. Renames resonances for consistency.
• st: Spectrum tool. Useful for global axes shift corrections (e.g. “referencing”).
• tb: Table of resonances for the project. Helps in identifying missing assignments.
• vc: View centering. Centers the view on a specific peak, especially useful when have associated peaks in 2D with 3D or 4D spectra.
• vd: View duplicate. Duplicates the view of a spectrum into another window.
• vR: Show assignments on the edge of the spectrum.
• vS: Show 1D slice on the edge of the spectrum.
• vz: Set the visible depth - useful for unfolding/unaliasing in the 4D HCNH NOESY.

Pointer Modes

• F1: Selection mode. Selects elements within the spectrum.
• F6: Add a label to your spectrum.
• F7: Draw a line, useful for marking or measuring.
• F8: Peak picking mode. Identifies peaks within the spectrum.
• F10: Integration mode. For integrating areas under peaks.
• F11: Zoom mode. Zoom in and out of specific areas of the spectrum.

Tips for Handling Peaks

When using the rp command to load a list of peaks, ensure the assignments follow the conventional format ([A-Z][0-9]+[A-Z0-9’]+-[A-Z0-9’]). For peaks with non-conventional names, consider using a custom script that modifies the .save file to ensure compatibility.