ℹ️ About this reference
Every command below can also be located at runtime with Command Finder (cf), which additionally searches POKY Notepad Scripts and POKY Notebooks — see POKY Notepad & POKY Notebooks below. For the full narrative feature list see the POKY Features page.
📋 On this page
- Core Built-in Commands
- Automated assignment
- Superfast assignment
- Chemical shift validation
- Structure calculation
- Structure prediction
- Large protein analysis
- Disordered protein analysis
- Perturbation analysis
- Nucleic acid analysis
- Small molecule analysis
- Solid-state NMR spectroscopy
- In silico screening
- Utilities
- Universal NMR formats
- About POKY
- General
- Assignment
- Integration
- Molecule
- Peak
- Spectrum
- Spectrum / Fold spectrum
- View
- Processing
- Selection
- Additional
- Reproducibility (Linux/macOS only)
- POKY Notepad & POKY Notebooks
Core Built-in Commands
These accelerators are wired directly into the POKY engine, independent of any Python extension. Many are described in more detail, with examples, on the Spectrum Views and Peaks & Assignments pages.
| Command | Description |
|---|---|
| at | Show assignment dialog |
| ot | Show ornament properties dialog |
| nt | Show ornament note dialog |
| yt / ya / yd | Show view synchronization dialog |
| pf | Show preferences dialog |
| pv | Show project view list dialog |
| pd | Show predefined resonances dialog |
| rr | Show rename resonances dialog |
| fo | Show spectrum open dialog |
| jo | Open a project |
| js | Save the current project |
| ja | Show project Save As dialog |
| jc | Close (unload) the current project |
| qt | Quit POKY |
| pm | Show easy access buttons (pointer mode toolbar) |
| ol | Show overlay dialog |
| eu | Undo the last edit (delete / integrate / move) |
| ra | Show resonance assignments dialog |
| r1 / r2 / r3 / r4 | Show resonance peak list for axis w1-w4 |
| sl | Show peak list of the current selection |
| cr | Show ornament color dialog |
| oz | Show ornament size dialog |
| ct | Show contour dialog |
| it | Show integration settings dialog |
| kt | Show peak pick settings dialog |
| tt / vt | Show view settings dialog |
| pt | Show print dialog |
| rt / rgX | Show region dialog |
| st | Show spectrum settings dialog |
| vz | Show view depth dialog |
| co | Show assignment copy dialog |
| mi | Show Midas dialog |
| tb | Show resonance/assignment table dialog |
| ag | Show assignment guessing dialog |
| Pb | Show POKY Structure Builder |
| Pa | Show POKY Structure Analyzer |
| Pn | Show POKY Notepad |
| PN | Show POKY Notebooks |
| Pv | Show PyMOL viewer |
| AO | About POKY dialog |
| LM | POKY license dialog |
| pc | Center selected peak(s) at local maximum |
| pe | Estimate linewidth of selected peak(s) |
| pg | Define a peak group from selected peaks |
| ph | Reset cached peak heights |
| pi | Integrate the selected peaks |
| pk / pu | Lock / unlock selected peaks |
| pa / pF / pP / pN | Select all / fully assigned / partially assigned / unassigned peaks |
| pC / pI / pA | Select by color / invert selection / select aliased peaks |
| pR / pS / pM / pL | Select intra-residue / sequential / medium-range / long-range assignments |
| pU | Unintegrate selected peaks |
| ac / ap / aP | Assignment copy / paste / paste (no overwrite) |
| aD | Delete assignments from selected peaks |
| aX | Crossdiagonal assignment copy |
| gs / ls / is / ps / xs / os | Toggle display of grids / labels / lines / peaks / peak groups / all ornaments |
| xd / xh / xp | Set axis units to index / Hz / ppm |
| xO | Set axis origin to pointer position |
| xr / xx | Roll / swap view axes |
| vc | Center view on the selected peak |
| vs / vb / xa | Toggle axis scales / scrollbars / nucleus-name display |
| vR / Vr | Toggle resonance panels (this view / all views) |
| vS / Vs | Toggle slice panels (this view / all views) |
| vC / Vc | Toggle contour scale (this view / all views) |
| VS / VB | Toggle axis scales / scrollbars for all views |
| vf | Toggle subtract-fit-peaks display |
| hh / ht / ho | Toggle crosshair / transposed crosshair / crosshair from other views |
| vd / vD / vh | Duplicate / destroy / hide the current view |
| vr | Redraw the current view |
| lu / lr / ll / lc | Unoverlap / right- / left- / center-align peak labels |
| lt / nl | Show peak list / new peak list window |
| rl | Show resonance list dialog |
| fa | Show spectrum Save As dialog |
| fs | Save the current spectrum |
| yr | Synchronize view ranges to match the current view |
| zp / zn / zr | Zoom to previous / next / remembered region |
| zi / zo / zf | Zoom in / out / full spectrum |
| zd / zu | Step one plane downfield / upfield (3D/4D) |
| a1-a4 / A1-A4 | Alias selected peaks down-/up-field along axis w1-w4 |
| d1-d4 / u1-u4 | Reflect selected peaks about the down-/up-field edge |
| ua | Remove alias from selected peaks |
| oc / op / oX | Ornament copy / paste / crossdiagonal copy |
| dr | Delete unused resonances |
| rv | Renumber the current view |
| ov / sc | Show orthogonal views |
| ib / ie / ig / il / iv | Set integration method: box / ellipse / Gaussian / Lorentzian / Voigt |
| mw | Toggle mouse wheel mode |
| RD | Set POKYHOME directory |
| 11 / 33 / 55 | Set pointer mode: select / peak / zoom |
💡 Raw key bindings: A handful of single-character keys
(+ - arrow keys
left/right/up/down and the bracket keys
[ ] ; ' { } : ") are bound directly for zoom, pan, and contour-level
nudging and are not listed individually here. See Cheat sheet from the main window.
Automated assignment
| Command | Description |
|---|---|
| ep | Run I-PINE automated assignment (PINE-SPARKY 2) |
| ip | Convert I-PINE to POKY resonance list file |
| oa | One Shot NMR Assignment |
| ar | Run ARSIGN automated sidechain assignment |
| pr | Pine assigner |
| pp | Pine graph assigner |
| ab | Assign the best by I-PINE |
| se | Select all floating I-PINE labels |
| EP | Run SSPINE automated assignment (ssPINE-POKY) |
| RP | Run N-HSQC peak matching |
Superfast assignment
| Command | Description |
|---|---|
| n3 | Superfast assignment with PACSY (about) |
| dg | Dummy graph |
| ta | Transfer and simulate assignments |
| ut | Untag _s |
| cu | Center and Untag _s |
| su | Select unconfirmed peaks with _s tag |
| mt | Merge two assignments to a pseudoatom |
| va | Versatile assigner |
| ti | 2D imaging for NMR strip operation via CV |
| CS | Chemical shift prediction by UCBShift |
| E1 | Chemical shift prediction by SHIFTX2 |
| CC | Chemical shift prediction by CASCADE |
| 1c | Simulate 1D peaks by CASCADE |
Chemical shift validation
| Command | Description |
|---|---|
| LA | Outlier detection and reference correction (about LACS) |
| lv | Run LACS validation |
| AA | NOESY-based assignment verification (about ARECA) |
| ea | Run ARECA chemical shift validator |
| AR | Use ARECA output list |
Structure calculation
| Command | Description |
|---|---|
| n4 | Automated structure calculation (about PONDEROSA) |
| c3 | Calculate 3D structure by PONDEROSA |
| up | Ponderosa Connector |
| gd | Generate Distance Constraints and White Lists |
| cy | Cyana2Sparky format |
| xe | XEASY, DYANA format |
| xf | Manual restraint format |
| en | eNORA 2 intensity file |
| sr | Phi-psi and accessible surface with STRIDE |
| hd | HADDOCK docking webserver |
| cw | CYRANGE webserver |
Structure prediction
| Command | Description |
|---|---|
| n6 | Run PECAN/CheSPI secondary structure prediction |
| gb | 2D structure prediction with GetSBY |
| gc | Secondary chemical shift analysis |
| gp | PACSY-ALIGN homology NOE assignment |
| ce | 3D structure prediction with CS-Rosetta (BMRB) |
| nm | NMR-like 3D structure prediction with PONDEROSA |
| af | AlphaFold 2 structure prediction |
| Af | AlphaFold 3 structure prediction |
| em | ESMFold structure prediction |
| bz | BOLTZ-2 structure prediction |
| ha | CHAI-1 structure prediction |
| DI | D-I-TASSER structure prediction |
| wa | Find peptide binders (Wazy and ColabFold) |
| IF | Binding site prediction (IF-SitePred) |
| OP | Order parameter prediction (OPPE) |
| tl | phi-psi prediction with TALOS-N (NIH or POKY) |
| tn | NDP-PLOT and PyMOL files using TALOS-N output |
| Ts | Torsion/SS/RCI/SASA prediction with TAPAS (POKY) |
| PP | Secondary structure prediction by PSIPRED (UCL) |
| SR | Secondary structure profiling by SSD-NMR (K. Zilm) |
| yo | Predict cysteine oxidation state |
| dp | Detect proline isomerization state |
| pK | Predict pKa using PDB (PROPKA 3) |
| cd | Circular dichroism analysis (BESTSEL) |
| fi | Predict disordered region interactions (FINCHES) |
Large protein analysis
| Command | Description |
|---|---|
| sn | Sidechain assignment with 4D-NOESY and CCH-TOCSY |
| MA | MAGIC-Act |
| MV | MAGIC-View |
| SN | PDB2NOE |
| un | UPL2NOE |
| NA | CYANA NOA Analysis |
| cy | Cyana2Sparky format |
| CY | Cyana2Sparky format colors |
Disordered protein analysis
| Command | Description |
|---|---|
| n8 | ncIDP-assign from Mulder Lab for IDP proteins (about) |
| RS | ncIDP Repositioner 1.2b |
| SG | ncIDP Spin Graph 1.2b |
| nc | ncSPC Propensity Calculator |
Perturbation analysis
| Command | Description |
|---|---|
| FA | Assign N-HSQC arbitrarily |
| np | NMR Perturbation Plot |
| ni | NMR Titration Plot |
| CF | CAFE — CSP mapping and Kd binding-affinity fitting |
| rh | Peak Height Analysis |
| PR | PRIDE — T1/T2/R1/R2, TauC/M.W., HetNOE, SEA-TROSY, TRACT, Model-Free, RCI/S² |
| LS | LISA — global 2D lineshape fitting for Kd/koff across an HSQC/HMQC/CPMG-HSQC titration series |
| eo | Easy overlay dialog |
| ec | Easy contour dialog |
| rd | RDC tool (RDC-POKY) |
| ch | CHESCA-SPARKY |
| cH | CHESPA-SPARKY |
| cO | CONCISE-POKY |
| sy | POKY-SYNCDYN |
Nucleic acid analysis
| Command | Description |
|---|---|
| N1 | Nucleic acid analysis (about RNA-PAIRS) |
| ER | Automated Imino Assignments (POKY's RNA-PAIRS) |
| SE | Show statistical ellipses for RNA analysis |
| DG | Dummy graph for nucleic acids |
| Ta | Transfer assignments to spectrum |
| NM | Nucleic acids modeler |
| MX | RNA secondary structure prediction by MXfold2 |
Small molecule analysis
| Command | Description |
|---|---|
| aa | A-SIMA: small molecule identification |
| am | A-MAP: metabolite analysis |
| PX | P-Mix — simulated-annealing compound mixture design for 1D NMR screening |
| LG | LigLib — lignin & cell wall model compound NMR shift library, peak matching, and assignment |
| CC | Chemical shift prediction by CASCADE |
| 1c | Simulate 1D spectrum by CASCADE |
| b1 | Simulate 1D spectrum by BMRB |
| 1b | Simulate 1D peaks by BMRB |
| ds | DeepSAT small molecule query by C-HSQC |
| CL | COLMAR-HSQC small molecule query by C-HSQC |
| oo | 1D projection inspector with overlay |
| Oo | 1D projection inspector with overlay (as 3D) |
| OO | 1D slice inspector with overlay |
Solid-state NMR spectroscopy
| Command | Description |
|---|---|
| PS | PISA-SPARKY automated PISA wheel analysis |
| EP | Run SSPINE automated assignment (ssPINE-POKY) |
| TA | Transfer and simulate assignments |
| ut | Untag _s |
| cu | Center and Untag _s |
| su | Select unconfirmed peaks with _s tag |
In silico screening
| Command | Description |
|---|---|
| po | POKY DOCK virtual screening |
| IF | Binding site prediction (IF-SitePred) |
| PX | P-Mix — simulated-annealing compound mixture design for 1D NMR screening |
Utilities
| Command | Description |
|---|---|
| ez | Export current project to single zip file |
| iz | Import from single zip file |
| do | Use clipboard to open many files at once |
| ae | Automated peak picking by APES |
| ca | Check protein assignment nomenclature |
| ck | Check resonance deviations |
| TB | Assignment table |
| cm | Assignment Completeness for Proteins (with a per-residue, per-atom-group completeness plot) |
| CM | Assignment Completeness for Nucleic Acids |
| ir | Import protein BMRB reference views |
| IR | Import RNA BMRB reference views |
| sq | Molecule sequence |
| rn | Renumber sequence indices |
| od | 1D inspector on NDPPlot |
| oo | 1D inspector with overlay |
| er | Convert XEASY prot to SPARKY resonance file |
| gx | Generate XEASY prot file |
| Pm | Generate a mmCIF (PDBx) file from a PDB file |
| Pp | Generate a PDB file from a mmCIF (PDBx) file |
| ah | Add hydrogens in a PDB file using REDUCE |
| MP | Evaluate a PDB ensemble using MolProbity |
| ri | Secondary structure of a PDB by STRIDE |
| DQ | PDB2PQR webserver |
| PB | APBS webserver |
| fP | Format PostScripts |
| dn | Deposit NMR data to BMRB |
| cf | Command finder |
| RD | Change POKYHOME |
| LF | Change look and feel |
| AI | AI Chat Assistant — chat with Claude, ChatGPT, or Gemini via their API, with live POKY session context |
Universal NMR formats
| Command | Description |
|---|---|
| ns | NMRSTAR 3.1 chemical shift to SPARKY resonance |
| es | Generate NMRSTAR 3.1 chemical shift file |
| bp | Parse NMRSTAR 3.2 file |
| bg | Generate NMRSTAR 3.2 file |
| ef | About NMR Exchange Format |
| e1 | Export sequence only to NEF |
| e2 | Export sequence and chemical shifts to NEF |
| i1 | NEF sequence to 3-letter-code format |
| i2 | NEF chemical shifts to Sparky resonance list |
| wo | Web version of Open Babel |
| xu | XEASY spectrum to UCSF spectrum |
About POKY
| Command | Description |
|---|---|
| n9 | About POKY |
| n0 | Citations... |
| nN | POKY webpage |
| TT | Video Tutorials |
| LC | NMRFAM-SPARKY Basics |
| SF | POKY user forum |
| dN | Download POKY software packages |
General
| Command | Description |
|---|---|
| py | Python shell |
Assignment
| Command | Description |
|---|---|
| ad | Assignment distances |
| MA | MAGIC-Act |
| MV | MAGIC-View |
| SN | PDB2NOE |
| un | UPL2NOE |
| NA | CYANA NOA Analysis |
| cy | Cyana2Sparky format |
| CY | Cyana2Sparky format colors |
| cs | Chemical shift plot |
| bm | Load BMRB STAR file |
| md | Mirror peak dialog |
| mp | Mirror peak show |
| na | Noesy assignment |
| rs | Reposition sequence |
| sg | Spin graph |
| ga | Spin graph assigner |
| cm | Assignment Completeness for Proteins (with a per-residue, per-atom-group completeness plot) |
| CM | Assignment Completeness for Nucleic Acids |
| ir | Import protein BMRB reference views |
| IR | Import RNA BMRB reference views |
| va | Versatile assigner |
| pq | PLUQin-POKY |
| lA | Label Assigned Peaks |
| bj | Build JSON Shifts |
Integration
| Command | Description |
|---|---|
| cl | Copy linewidths |
| lp | Linewidth plot |
| rh | Relaxation peak heights |
| ve | Volume errors |
Molecule
| Command | Description |
|---|---|
| ax | Atom name translation |
| mc | Midas constraints |
| ma | Midas atom picking |
| sq | Molecule sequence |
| SA | Sequence alignment |
| pn | PDB atom names |
| mg | Make ensemble from PDBs |
| mx | Make ensemble from XPLOR run |
| fe | Fit ensemble |
Peak
| Command | Description |
|---|---|
| hc | HC peaks |
| SL | List selected peaks |
| dd | Delete duplicate peaks |
| mf | MARDIGRAS format |
| LT | Peak list |
| pb | Peak table |
| rp | Read peak list |
| kr | Restricted peak pick |
| mv | Shift resonances |
| tf | TALOS format |
| qn | Add single quote note |
| v3 | Show 3D peaks |
| p3 | Project a 3D peak onto 2D |
| TP | Transfer a peak |
| cc | Coupling constants |
| xe | XEASY, DYANA format |
| xf | Manual restraint format |
| z5 | IDAP 1D NMR |
| zs | Display heights as a function of data point |
| iP | iPick peak picker |
| re | REDEN peak decomposition |
Spectrum
| Command | Description |
|---|---|
| al | Align spectrum |
| cx | CORMA spectrum |
| fm | Open multiple files |
| la | Spectrum labelled axis |
| rm | Spectrum region RMSD |
| dc | Default contour levels |
| CO | Add or subtract two spectra |
| WD | Wavelet denoising of a spectrum |
| DR | Spectral dimension reduction |
| DH | Scale data heights |
| S2 | Slice 2D planes from a 3D spectrum |
| bs | Simulate 2D spectrum with BMRB |
| me | Simulate a practice set (SIM-PRAC) |
| mr | Make a simulated and a residual spectra |
| bb | BLASTP BMRB entries |
| RM | Rank Predicted Models by NMR (RPM-NMR) |
Spectrum / Fold spectrum
| Command | Description |
|---|---|
| f1 | Add w1 sweepwidth (alias peak) |
| f2 | Add w2 sweepwidth (alias peak) |
| f3 | Add w3 sweepwidth (alias peak) |
| f4 | Add w4 sweepwidth (alias peak) |
| F1 | Subtract w1 sweepwidth (alias peak) |
| F2 | Subtract w2 sweepwidth (alias peak) |
| F3 | Subtract w3 sweepwidth (alias peak) |
| F4 | Subtract w4 sweepwidth (alias peak) |
View
| Command | Description |
|---|---|
| cv | Center view setup |
| rx | Reflection crosshair |
| sp | Strip plot |
| SP | Additional strip plot |
| Sp | Another additional strip plot |
| dh | Draw a center horizontal line |
| dv | Draw a center vertical line |
| tc | Type center chemical shifts |
| uc | Uniform contour settings |
| us | Uniform view sizes |
| uv | Uniform view extents |
| on | Organize neighboring views |
| TH | Tile horizontal |
| TV | Tile vertical |
| TG | Tile grid |
| da | Auto-adjust view ratio by peaks |
| PV | Filterable View List |
| tv | Tree View |
| ng | NMRGlue Plot |
| 3p | 3D Perspective Plot |
Processing
| Command | Description |
|---|---|
| PY | Proky — Quick Convert, Process 1D, Batch Process 1Ds, Process nD, NMRPipe + Phaser 2D, Pseudo-2D T1/T2, Import 1D Format |
| P! | Process 1D with Phaser 1D |
| P@ | Process 1Ds with Phaser 1D |
| P1 | Process nD with Phaser 1D |
| P2 | Process nD with Phaser 2D |
Selection
| Command | Description |
|---|---|
| AS | Advanced Selection |
| sb | Select bigger peaks |
| ss | Select smaller peaks |
| SB | Select same sign bigger peaks |
| SS | Select same sign smaller peaks |
| sF | Select all floating labels |
| sL | Select all labels attached to peaks |
| sO | Select all ornaments |
| sG | Select all grids |
| sN | Select all lines |
| sA | Select all assigned peaks |
| Sa | Select all unassigned peaks |
| sB | Select all user-labeled peaks |
| Sb | Select all non-user-labeled peaks |
| su | Select unconfirmed peaks with _s tag |
| uP | Unselect all peaks |
| Sl | Select labels of selected peaks |
| Sg | Select by groups (a.a., b.p.) |
| pV | Select visible peaks |
| Lv | Select visible labels |
Additional
| Command | Description |
|---|---|
| ms | Mouse chemical shift |
| ob | Open from clipboard... |
Reproducibility (Linux/macOS only)
| Command | Description |
|---|---|
| aU | About UCONN Connjur |
| rE | Snapshot dialog |
| rG | Group dialog |
POKY Notepad & POKY Notebooks
Beyond the two-letter command menus above, POKY ships two scriptable automation surfaces. Both are indexed by Command Finder (cf) alongside every menu accelerator, so a single search box covers all three command sources.
POKY Notepad (Pn)
POKY Notepad (Pn) is the built-in script editor for
batch tasks — write or load a Python script, run it against the active project, and see
output and errors inline. POKY Notepad Scripts are a curated, growing library
of ready-made scripts hosted in the
pokynmr/POKY GitHub repository,
under the User_Modules/ and PokyNotepad_Scripts/ directories.
Command Finder downloads the current script list and lets you search and load any of them
directly into Notepad without leaving POKY.
POKY Notebooks (PN)
POKY Notebooks (PN) are Jupyter notebook workflows
distributed alongside POKY in the
Jupyter_Notebooks
directory of the same repository. Command Finder reads the notebook index
(Jupyter_Notebooks/files_list.json) and opens any matching .ipynb
notebook directly in your browser.
Command Finder (cf)
Open Command Finder with cf and type any keyword. Results are merged from three sources and labeled accordingly:
| Result prefix | Source | Action on double-click |
|---|---|---|
| (none — menu label) | Any two-letter command currently registered in the POKY menu bar | Executes the command, as if typed in a spectrum view |
POKY Notebooks: | Jupyter_Notebooks/files_list.json in the POKY GitHub repository | Opens the notebook URL in your browser |
POKY Scripts: | User_Modules/ and PokyNotepad_Scripts/ in the POKY GitHub repository | Downloads the script and opens it in POKY Notepad |
💡 Requires internet access: POKY Notebook and POKY Notepad Script
results are fetched live from GitHub each time Command Finder builds its list — without
a connection, only the local two-letter menu commands are searchable.