# Command Index

## Input

- Processed NMR data
  - NMRPipe
  - Felix
  - Varian VNMR
  - Bruker XWinNMR and UXNMR
- UCSF NMR format
- Sparky spectrum annotation (aka "save") files
- Sparky project files

## Output

- Peak lists
- Chemical shift list
- Chemical shift table

## File commands

file open... | fo | open UCSF NMR data, a Felix matrix, or a Sparky spectrum file
file save | fs | save a Sparky spectrum annotation file
file save as... | fa | save spectrum with a new name
project open... | jo | open several spectra at once
project save | js | save all spectra
project save as... | ja | save project with a new name
preferences... | pf | miscellaneous settings
quit | qt

## View commands

axes in Hertz | xh | display view scale axes in Hz
axes in ppm | xp | display view scale axes in parts per million
axes show index | xd | show data index values on view scales
axis nucleus types | xa | show nucleus type (1H, 13C, 15N) on axes
axis roll | xr | exchange axes keeping center point of fixed
axis transpose | xx | zoom to cross-diagonal region of spectrum
center view on peak | vc | center a view on the selected peak
orthogonal views | ov | show 3 orthogonal views of a 3-D spectrum
region goto | rg | zoom to a named region
region tool... | rt | name regions of a spectrum
renumber view | rv | renumber view name to use lowest available suffix number
show axis scales | vs | show scales (ppm, hz, or index units) along view axes
show grids | gs | toggle display of grids
show labels | ls | toggle display of labels
show lines | is | toggle display of lines
show ornaments | os | toggle display of all ornaments
show peaks | ps | toggle display of peaks
show peak groups | xs | toggle display of peak groups
show peak info | vp | show peak position / height / linewidth in status bar
show resonances | vR | show resonances along edge of spectrum
show scrollbars | vb | show scrollbars for view windows
show slices | vS | show 1-D data cross-sections along edge of spectrum
view duplicate | vd | make another view window
view hide | vh | undisplay a view
view redraw | vr | redraw the view (in case it gets messed up)
view settings... | vt | set crosshairs, aspect ratio, slices, ...
zoom full | zf | show entire spectrum
zoom in | zi | zoom in by a factor of 2
zoom out | zo | zoom out by a factor of 2
zoom down | zd | move down a plane in a 3D spectra
zoom up | zu | move up a plane in a 3D spectra
zoom previous | zp | zoom to the previously shown region
zoom next | zn | reverse of zoom previous (zp) command

## Peak commands

add sweepwidth | a1 a2 a3 a4 | adjust peak w1,w2,w3,w4 frequency one sweepwidth downfield
subtract sweepwidth | A1 A2 A3 A4 | adjust peak w1,w2,w3,w4 frequency one sweepwidth upfield
reflect upfield | u1 u2 u3 u4 | reflect peak w1,w2,w3,w4 frequency about upfield boundary
reflect upfield | d1 d2 d3 d4 | reflect peak w1,w2,w3,w4 frequency about downfield boundary
assignment copy | ac | remember peak assignments for assignment paste
assignment delete | aD | delete the assignments of selected peaks
assignment paste | aP | paste assignments onto peaks in this spectrum
assignment paste & label | ap | copy assignments and show labels
crossdiagonal assignment copy | aX | copy assignments from crossdiagonal peaks
assignment tool... | at | make assignments
delete unused resonances | dr | delete resonances not used in any peak assignments
integration tool... | it | select integration method
sum over box method | ib | switch to box integration method
sum over ellipse method | ie | switch to ellipse integration method
Gaussian fit method | ig | switch to Gaussian fit integration
Lorentzian fit method | il | switch to Lorentzian fit integration
integrate selected peaks | pi
ornament copy | oc | record ornaments for future paste operation
ornament paste | op | paste ornaments into this spectrum
crossdiagonal ornament copy | oX | copy ornaments across diagonal of 2D homonuclear spectrum
center peaks | pc | center selected peaks at local maxima or minima.
estimate linewidths | pe | get linewidth of selected peaks as width at half max
group peaks | pg | create a peak group from selected peaks
update heights | ph | reread peak heights from NMR data file
label peak | pl | put a label on a peak using a dialog
label peaks | lb | put assignment labels on selected peaks
unlabel peaks | lB | Remove labels from selected peaks
unoverlap labels | lu | move labels so they don't overlap each other
right offset labels | lr | move labels so they are to the right of peak markers
lock peaks | pk | prevent peaks from moving when integrated
select all peaks | pa | select all peaks in a spectrum
select fully assigned | pF | select fully assigned peaks
select partially assigned | pP | select partially assigned peaks
select unassigned | pN | select unassigned peaks
select by color | pC | select peaks by color
invert peak selection | pI | invert peak selection
select aliased | pA | select aliased peaks
select intra-residue | pR | select i to i assigned peaks
select sequential | pS | select i to i+1 assigned peaks
select medium range | pM | select i to i+2, i+3 or i+4 assigned peaks
select long range | pL | select i to i+5, i+6, ... assigned peaks
unintegrate peaks | pU | forget that a peak has been integrated
unlock peaks | pu | allow selected peaks to move when integrated
undo | eu | undo last peak move, deletion, or integration
w1 resonance peaks | r1 | list assigned peaks with selected peak w1 resonance
w2 resonance peaks | r2 | show assigments with selected peak w2 resonance
w3 resonance peaks | r3 | show assigments with selected peak w3 resonance

## Dialogs

assignment... | at | make assignments
assignment copy... | co | thresholds for copying assignments
assignment table... | tb | table of chemical shifts
contour levels... | ct | set contour levels and colors
integration... | it | set integration method
midas... | mi | display assignments on a structure using Midas
ornament... | ot | change ornament colors and sizes
note... | nt | add notes to peaks
overlay views... | ol | overlay contours of one spectrum on another
peak list... | lt | show a list of peaks for a spectrum
peak picking... | kt | set thresholds for find peak pointer mode
pointer modes... | pm | show buttons to select pointer mode
predefined resonances... | pd | copy resonances from another spectrum
preferences... | pf | set global Sparky options
print view... | pt | print spectrum views to a Postscript printer
project view list... | pv | list of views, sizes, peak counts, ...
python... | py | Python shell for running your own programs
region... | rt | name regions and apply operations to regions
rename resonances... | rr | rename atoms and groups
resonance list... | rl | list group/atom chemical shifts, standard deviations
spectrum... | st | set molecule and condition, and axis shifts
synchronize views... | yt | make views scroll in parallel
view... | vt | options controlling what is displayed in a view

## Pointer Modes

select | F1 | click or drag to select or move peaks, labels, lines, ...
center | F2 | clicking centers view on point
add grid both | F3 | place vertical and horizontal grid lines
add grid horz | F4 | add a line extending across whole spectrum
add grid vert | F5 | add a line extending across whole spectrum
add label | F6 | add a text label to a peak
add line | F7 | add a horizontal or vertical line between end points
find / add peak | F8 | click to place a peak or drag to find peaks
integrate | F10 | click or drag to integrate peaks
zoom | F11 | drag to select a new region to show
duplicate and zoom | F12 | drag to zoom and duplicate a view
assignment copy | sh-F1 | copy assignments from an already assigned spectrum
assignment guess | sh-F2 | make assignment if there is a unique guess