Sparky is the most popular NMR analysis tool for biomolecules for more than a decade. NMRFAM has taken over the original Sparky from UCSF for the continuous development to implement advances in biomolecular NMR field. Thanks to the generous allowance of Tom Goddard and Tom Ferrin from UCSF, NMRFAM is official center for developing, maintaining and distributing the new version of Sparky that we call it NMRFAM-SPARKY.
SPARKY (https://www.cgl.ucsf.edu/home/sparky) remains the most popular computer program for NMR operations, such as peak-picking and peak assignment, despite that fact that its originators have not released a new version since 2001 (Goddard & Kneller, SPARKY 3).
SPARKY supports user-defined enhancements, and we have used these to develop new tools in support of our packages for automated protein assignment and structure determination.
The added features support
(1) interfacing with servers offering new technologies,
(2) tools for data visualization and verification, and
(3) new protocols for maximizing the efficiency of NMR data analysis.
We have refined these SPARKY enhancements through their use in our annual workshops by participants with varying experience in protein NMR spectroscopy. We describe here the new package, which we have named “NMRFAM-SPARKY”.
NMRFAM-SPARKY Available for Download
The following distributions have been created for download. NMRFAM-SPARKY is not required to be explicitly installed on the host operating system. To run the program, simply unpack the binary, navigate to the bin directory where the Sparky launch script is present, and execute the launch script.
|Platform||Binary||Archive Format||Launch Script|
|Linux 32/64 bit||nmrfam-sparky-linux.tar.gz||gzip tar file||bin/sparky|
|Mac OS X (10.7 or newer)
||nmrfam-sparky-mac.tar.gz||gzip tar file||NMRFAM-SPARKY.app|
NMRFAM-SPARKY 1.3 powered by Sparky 3.12
- Sparky version = 3.12
- Python (bundled) version = 2.7, Tcl/Tk version = 8.6 (Win/Linux), 8.5 (Mac)
- NMRFAM extensions version = 1.3
|Automated assignment||n1|| >>>
Automated BB and SC assignment: PINE
Open PINE web page for automatic resonance assignment.
PINE(BMRB) input files. Generate peak list and assignment files
that are readily acceptable for PINE, and open PINE web page.
||Convert PINE automated assignments into Sparky ornaments. Related commands (see below) can be used to accept a probabilistic assignment as a "hard" assignment in Sparky|
||PINE sequence formatting. Convert various sequence formats to PINE sequence format (3-letter-code).|
Open PINE-SPARKY original web page for quick tutorial.
converter. Automatically detect and launch PINE2SPARKY
converter for PINE outputs to be imported to NMRFAM-SPARKY.
|ab||Assign the best by
PINE. Accept all candidate assignments by PINE that are greater
than a threshold probability.
|pp||Pine Graph Assigner. Graphically examine all assignments and probable candidates on a per residue & atom by atom basis.|
|pr||Pine Assigner. Accept all automated assignments on a peak by peak basis.|
|se||Select all floating
labels. PINE labels are not linked to an actual peak. They can
be selected by using this function to be removed.
Superfast side chain assignment
Superfast assignment on-the-fly referring PACSY
Graphically examine all assignments on a per residue & atom by atom
basis without PINE runs.
simulate assignments. Transfer or simulate assignments to
different experiments. Simulated assignments will have "_s" tag after
Detach "_s" tag indicating simulation generated by "ta" two-letter
|cu||Center and Untag _s.
Move a peak to the local maximum and detach "_s" tag.
|mt||Merge two assignments
to a pseudoatom. When two probable pseudo-assigned peaks are at the
same position, drop a last numeric character from one assignment while
the other is selected to delete.
Wishart Lab. Open SHIFTX2 web server for chemical shift
|Chemical shift validation
||>>> Assignment outlier detection and correction of errors in referencing: LACS
||Run LACS validation. Submit a LACS chemical shift validation to detect outliers and possible error corrections.
||>>> Assessment of the reliability of chemical shift assignments: ARECA
||Export to ARECA input files. Generate ARECA input files and open ARECA web page to assess chemical shift assignment quality by NOESY peak lists.|
||ARECA list. Sort of peak list handling ARECA output for estimating your assignment confidence.|
Automated structure calculation: PONDEROSA
Open PONDEROSA-C/S web page
3D structure by
PONDEROSA. Identify NOE peaks and submit a calculation to
the Ponderosa Server with PONDEROSA-X refinement option. Ponderosa
Client is not necessary to run this function.
Client. Automatically detect and launch Ponderosa Client for
fully automated NOE assignment, torsion angle prediction,
structure calculation and refinement.
|up||Update Ponderosa. Open
a connection window for validating PONDEROSA-C/S outputs
Generate Distance Constraints / Whitelists for PONDEROSA. Open a dialog to select NOESY spectra to generate distance constraints in .upl and .lol format. These files can be used by both PONDEROSA and CYANA. Close residue contact information will be saved as whitelists (.wlt) format acceptable for PONDEROSA.
|Module for conversions of chemical shifts list and peak lists between Sparky and the structure analysis program Cyana. This module extends the original xeasy (xe) command of the original Sparky distribution by adding import functionality and conversion between pseudoatom nomenclatures used by Cyana and standard IUPAC conventions.|
Imports a Cyana peak list (XEASY format) into Sparky. Conversion between
Cyana pseudoatom nomenclatures and standard IUPAC nomenclatures is automatically performed.
* Under NMRFAM -> Automated structure calculation
|xe||XEASY, CYANA format. Export NOESY peak lists to Xeasy format with optional Cyana header and conversion of IUPAC pseudoatom nomenclatures to Cyana-compatible names. Checkbox can be used to turn on/off Cyana-specific formatting and nomenclature substitution.|
||Manual restraint format. Create distance restraints in Xplor/Cyana/Ponderosa format.
||Extract phi-psi and
accessible surface info from PDB by STRIDE. Open STRIDE web server for
PDB structural analysis.
||n5||>>> Structural predictions
|n6||Run PECAN 2D structure prediction. Generate PECAN input file and run PECAN web server to receive secondary structure prediction.
||2D structure prediction with GetSBY. Run GetSBY 2D structure prediction. GetSBY is based on quantification of PACSY DB.
||Secondary chemical shift analysis. Compare secondary chemical shifts by referencing coil chemical shifts from PACSY DB.
||Export to PACSY-ALIGN and PACSY-ALIGN web server. Generate NMR-STAR 3.1 file and open PACSY-ALIGN web page to find similar proteins and generate NOESY assignments.|
structure prediction. Generate CS-Rosetta input file (TALOS
format) and open CS-Rosetta web service page powered by HTCondor (BMRB).
with TALOS-N (NIH). Generate TALOS input file and open TALOS-N
web service page supported by NIH for torsion angle prediction.
prediction with PSIPRED (UCL). Open PSIPRED web server.
|Large protein analysis
||>>> SCAssign from Yang Lab for large proteins|
assignment with 4D-NOESY and CCH-TOCSY. Run SCAssign
extension developed from Prof. Yang Daiwen's group at NUS. Instructions
can be found at [here]
|Disordered protein analysis
||>>> ncIDP-assign from Mulder Lab for IDP proteins
Reposition assigned stretch of protein sequence using ncIDP chemical
|SG||ncIDP Spin Graph.
Generate resonance and peak assignments for IDP proteins using sequence
and peak lists for several spectra.
arbitrarily. In many case you do perturbation study, assignments
are required. This function generates assignments starting from residue
number 1. They can be copied to the other N-HSQC sets by ornament copy
function (two-letter-code: "oc" and "op")
Plot. This function is for comparing global dynamic properties
of two spectra including chemical shifts, intensities, line widths,
volumes, et al. This requires matching assignments on both spectra.
||NMR Titration Plot.
This function is for comparing local dynamic properties of multiple
spectra. This works for chemical shift titration depending on user
heights. This function is enhanced from original Sparky. If
peaks are assigned, they will be sorted by sequence indices. New
plotting program is adapted in the curve fit window.
||Easy overlay dialog. Open an easy overlay dialog that allows user can set overlaid views by mostly mouse clicks very efficiently.
||Easy contour dialog.
Open an easy contour dialog that allows user can set contour settings
of multiple spectra by mostly mouse clicks very eficiently.
|Nucleic acid analysis
||Export to RNA-PAIRS.
RNA-PAIRS (RNA Probabilistic Assignment of Imino Resonance Shifts) is a
web server assigning chemical shifts of RNA imino groups. This feature
exports users to select two spectra (N-HSQC and HH-NOESY) for RNA-PAIRS
into user selected directory and opens RNA-PAIRS web page for
ellipses for RNA analysis. Draw ellipses on RNA spectrum to
guide chemical shift assignment and analysis of nucleic acids.
||Dummy graph for
nucleic acids. Open an interactive window visualizing
assignments and atomic structures of nucleic acids.
||Drag and copy to open multiple spectra. Drag and copy in the file manager (Explorer, Finder, Nautilus), and paste in the window to open multiple spectra at once.
picking by APES.
Open a dialog for an advanced peak picking for backbone spectra.
||Check protein assignment nomenclature. Open a dialog for checking and fixing nomenclature errors.|
indices. Batch sequence renumbering by setting new first index
of the sequence. Type "dr" before and after this
function is necessary to remove unused resonances.
||1D inspector. Plot 1D slice of selected integrated peaks in NDP-Plot.
3.1 to SPARKY. Convert NMR-STAR 3.1 formatted chemical shift
file from BMRB to SPARKY resonance list file.
||Generate NMR-STAR 3.1 file. Generate NMR-STAR 3.1 formatted chemical shift file from current chemical shift assignments.
|er||Convert XEASY prot to SPARKY. Convert XEASY prot chemical shift file to SPARKY resonance list file.
Execute a batch program to convert multiple NMRPIPE files to SPARKY
|Bu||Run easy_bruk2ucsf. Execute a batch program to convert multiple Bruker 2rr files to SPARKY files.|
Save SPARKYHOME variable as sparkyhome.cfg in the user directory. The
file is read when NMRFAM-SPARKY is booted to set the root directory for
Project, Save and Spectra sub-directories.
Export sequence to NEF format.
||Export sequence and chemical shifts. Export sequence and chemical shifts to NEF format.|
NEF sequence to .seq file. Extract sequence from NEF and create
||Convert NEF chemical shifts to
Sparky resonance list. Extract chemical shifts from NEF and
create Sparky resonance list file to read in by two-letter-code "rl".
|HC Peaks||hc||Modifications to original Sparky extension that places peak
markers on a 2D 1H-13C HSQC spectrum using
|Strip Plot||sp||Modifications to original Sparky extension dialog for
creating strip plots.
|Select by heights
||Select bigger peaks than currently selected peak in the spectrum.
||Select smaller peaks than currently selected peak in the spectrum.|
||Select bigger same signed peaks than currently selected peak in the spectrum.|
||Select smaller same signed peaks with same sign than currently selected peak in the spectrum.|
Treatment of Non Standard Pseudoatom Nomenclatures
In order to both assist and enable IUPAC nomenclatures for atoms to be consistently used within Sparky when using the structure calculation program CYANA, NMRFAM made the following changes to Sparky extensions:
- Any valid IUPAC names missing from the 'atomnames.py' file were added to its data structures. This enables all peaks with pseudoatom conventions to be transferred to a 2D 1H-13C HSQC spectrum using the 'hc' command.
- Upon export from Sparky to Cyana, IUPAC atom names are replaced with Cyana-compatible names "on-the-fly".
- Upon import to Sparky from Cyana, all non-standard atom names are replaced with their IUPAC convention
- NMRFAM-SPARKY citation:
Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.
Lee W, Tonelli M, Markley JL
- PINE-SPARKY citation
Bioinformatics. 2009 Aug 15;25(16):2085-7. Epub 2009 Jun 3.
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.
Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL.
- PACSY citation
J Biomol NMR. 2012 Oct;54(2):169-79
PACSY, a relational database management system for protein structure and chemical shift analysis.
Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL.
- PINE citation
PLoS Comput Biol. 2009 Mar;5(3):e1000307.
Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy.
Bahrami A, Assadi AH, Markley JL, Eghbalnia HR.
- PECAN citation
J Biomol NMR. 2005 May;32(1):71-81.
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
Eghbalnia HR1, Wang L, Bahrami A, Assadi A, Markley JL.
- PONDEROSA citation
J Biomol NMR. 2014 Sep 5.
PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.
Lee W, Stark JL, Markley JL.
Bioinformatics. 2011 Jun 15;27(12):1727-8.
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.
Lee W, Kim JH, Westler WM, Markley JL.
- APES citataion
Expert Rev Proteomics. 2008 Aug;5(4):589-601.
Structural proteomics by NMR spectroscopy.
Shin J, Lee W, Lee W.
- GetSBY citation
Lee W, Lee W. Method to predict protein secondary structure using NMR spectroscopy. The Korean Intellectual Property Office. 2009 Mar 16. Reg. No.: 1008899400000
Expert Rev Proteomics. 2008 Aug;5(4):589-601.
Structural proteomics by NMR spectroscopy.
Shin J, Lee W, Lee W.
- SPARKY 3 citation
Goddard TD & Kneller DG (2008) SPARKY 3. University of California, San Francisco.
- SHIFTX2 citation
J Biomol NMR. 2011 May;50(1):43-57
SHIFTX2: significantly improved protein chemical shift prediction.
Han B, Liu Y, Ginzinger SW, Wishart DS.
- STRIDE citataion
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W500-2.
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.
Heinig M, Frishman D.
- TALOS-N citation
J Biomol NMR. 2013 Jul;56(3):227-41.
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Shen Y, Bax A.
- CS-Rosetta citation
Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4685-90.
Consistent blind protein structure generation from NMR chemical shift data.
Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A.
- PSIPRED citation
J Mol Biol. 1999 Sep 17;292(2):195-202.
Protein secondary structure prediction based on position-specific scoring matrices.
- SCAssign citation
Bioinformatics. 2006 Nov 15;22(22):2833-4.
SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labeled large proteins.
Zhang L, Yang D.
- ncIDP-assign citation
Bioinformatics. 2011 Apr 1;27(7):1039-40.
ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
Tamiola K, Mulder FA.
- RNA statistical ellipses citation
Nucleic Acids Res. 2013 Oct;41(18):e172.
Automated and assisted RNA resonance assignment using NMR chemical shift statistics.
Aeschbacher T, Schmidt E, Blatter M, Maris C, Duss O, Allain FH, Güntert P, Schubert M.
As Sparky accepts additional plug-ins written in Python, we are happy to include your contributions in the next version of NMRFAM-SPARKY.
Please contact Dr. Woonghee Lee (firstname.lastname@example.org) for details.