Skip to main content
SpringerLink
Log in

PR-CALC: A Program for the Reconstruction of NMR Spectra from Projections

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

Projection-reconstruction NMR (PR-NMR) has attracted growing attention as a method for collecting multidimensional NMR data rapidly. The PR-NMR procedure involves measuring lower-dimensional projections of a higher-dimensional spectrum, which are then used for the mathematical reconstruction of the full spectrum. We describe here the program PR-CALC, for the reconstruction of NMR spectra from projection data. This program implements a number of reconstruction algorithms, highly optimized to achieve maximal performance, and manages the reconstruction process automatically, producing either full spectra or subsets, such as regions or slices, as requested. The ability to obtain subsets allows large spectra to be analyzed by reconstructing and examining only those subsets containing peaks, offering considerable savings in processing time and storage space. PR-CALC is straightforward to use, and integrates directly into the conventional pipeline for data processing and analysis. It was written in standard C+ + and should run on any platform. The organization is flexible, and permits easy extension of capabilities, as well as reuse in new software. PR-CALC should facilitate the widespread utilization of PR-NMR in biomedical research.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • H.S. Atreya A. Eletsky T. Szyperski (2005) J. Am. Chem. Soc. 127 4554–4555 Occurrence Handle10.1021/ja042562e

    Article  Google Scholar 

  • H.S. Atreya T. Szyperski (2005) Methods Enzymol. 394 78–108

    Google Scholar 

  • C. Bartels T.-H. Xia M. Billeter P. Güntert K. Wüthrich (1995) J. Biomol. NMR 5 1–10

    Google Scholar 

  • R.N. Bracewell (1956) Aust. J. Phys. 9 198–217 Occurrence Handle1956AuJPh...9..198B Occurrence Handle0071.21304 Occurrence Handle18,179e

    ADS  MATH  MathSciNet  Google Scholar 

  • R.N. Bracewell (2000) The Fourier Transform and Its Applications McGraw-Hill Boston

    Google Scholar 

  • R.N. Bracewell A.C. Riddle (1967) Astrophys. J. 150 427–434 Occurrence Handle1967ApJ...150..427B Occurrence Handle10.1086/149346

    Article  ADS  Google Scholar 

  • B. Brutscher F. Cordier J.P. Simorre M.S. Caffrey D. Marion (1995) J. Biomol. NMR 5 202–206 Occurrence Handle10.1007/BF00208811

    Article  Google Scholar 

  • B.E. Coggins R.A. Venters P. Zhou (2004) J. Am. Chem. Soc. 126 1000–1001 Occurrence Handle10.1021/ja039430q

    Article  Google Scholar 

  • B.E. Coggins R.A. Venters P. Zhou (2005) J. Am. Chem. Soc. 127 11,562–11,563 Occurrence Handle10.1021/ja053110k

    Article  Google Scholar 

  • S.R. Deans (1983) The Radon Transform and Some of Its Applications John Wiley & Sons New York

    Google Scholar 

  • F. Delaglio S. Grzesiek G.W. Vuister G. Zhu J. Pfeifer A. Bax (1995) J. Biomol. NMR 6 277–293 Occurrence Handle10.1007/BF00197809

    Article  Google Scholar 

  • K. Ding A.M. Gronenborn (2002) J. Magn. Reson. 156 262–268 Occurrence Handle2002JMagR.156..262D Occurrence Handle10.1006/jmre.2002.2537

    Article  ADS  Google Scholar 

  • R. Freeman E. Kupče (2003) J. Biomol. NMR 27 101–113 Occurrence Handle10.1023/A:1024960302926

    Article  Google Scholar 

  • R. Freeman E. Kupče (2004) Concept. Magnetic. Res. 23A 63–75

    Google Scholar 

  • L. Frydman A. Lupulescu T. Scherf (2002) Proc. Natl. Acad. Sci. U.S.A. 99 15,859–15,862 Occurrence Handle10.1073/pnas.252644399

    Article  Google Scholar 

  • Goddard, T.D. and Kneller, D.G. SPARKY 3, University of California, San Fransisco.

  • S. Hiller F. Fiorito K. Wüthrich G. Wider (2005) Proc. Natl. Acad. Sci. U.S.A. 102 10,876–10,881 Occurrence Handle10.1073/pnas.0504818102

    Article  Google Scholar 

  • J.C. Hoch A.S. Stern (1996) NMR Data Processing Wiley-Liss New York

    Google Scholar 

  • J.C. Hoch A.S. Stern (2001) Methods Enzymol. 338 159–178

    Google Scholar 

  • H. Hu A.A. Angelis Particlede V.A. Mandelshtam A.J. Shaka (2000) J. Magn. Reson. 144 357–366 Occurrence Handle2000JMagR.144..357H Occurrence Handle10.1006/jmre.2000.2066

    Article  ADS  Google Scholar 

  • L. Jiang B.E. Coggins P. Zhou (2005) J. Magn. Reson. 175 170–176 Occurrence Handle2005JMagR.175..170J Occurrence Handle10.1016/j.jmr.2005.03.014

    Article  ADS  Google Scholar 

  • B.A. Johnson R.A. Blevins (1994) J. Biomol. NMR 4 603–614 Occurrence Handle10.1007/BF00404272

    Article  Google Scholar 

  • A.C. Kak M. Slaney (1999) Principles of Computerized Tomographic Imaging IEEE Press New York

    Google Scholar 

  • L.E. Kay P. Keifer T. Saarinen (1992) J. Am. Chem. Soc. 114 10,663–10,665 Occurrence Handle10.1021/ja00052a088

    Article  Google Scholar 

  • S. Kim T. Szyperski (2003) J. Am. Chem. Soc. 125 1385–1393

    Google Scholar 

  • E. Kupče R. Freeman (2003a) J. Magn. Reson. 162 300–310 Occurrence Handle2003JMagR.162..300K

    ADS  Google Scholar 

  • E. Kupče R. Freeman (2003b) J. Am. Chem. Soc. 125 13,958–13,959

    Google Scholar 

  • E. Kupče R. Freeman (2003c) J. Biomol. NMR 27 383–387

    Google Scholar 

  • E. Kupče R. Freeman (2004a) J. Biomol. NMR 28 391–395

    Google Scholar 

  • E. Kupče R. Freeman (2004b) J. Am. Chem. Soc. 126 6429–6440

    Google Scholar 

  • E. Kupče R. Freeman (2004c) Concepts Magn. Reson. 22A 4–11

    Google Scholar 

  • E. Kupče R. Freeman (2005) J. Magn. Reson. 173 317–321 Occurrence Handle2005JMagR.173..317K

    ADS  Google Scholar 

  • D. Malmodin M. Billeter (2005a) Prog. Nucl. Magn. Reson. Spectrosc. 46 109–129

    Google Scholar 

  • D. Malmodin M. Billeter (2005b) J. Am. Chem. Soc. 127 13,486–13,487 Occurrence Handle10.1021/ja0545822

    Article  Google Scholar 

  • D. Malmodin M. Billeter (2005c) J. Magn. Reson. 176 47–53 Occurrence Handle2005JMagR.176...47M Occurrence Handle10.1016/j.jmr.2005.05.020

    Article  ADS  Google Scholar 

  • V.A. Mandelshtam (2000) J. Magn. Reson. 144 343–356 Occurrence Handle2000JMagR.144..343M Occurrence Handle10.1006/jmre.2000.2023

    Article  ADS  Google Scholar 

  • H.N.B. Moseley N. Riaz J.M. Aramini T. Szyperski G.T. Montelione (2004) J. Magn. Reson. 170 263–277 Occurrence Handle2004JMagR.170..263M Occurrence Handle10.1016/j.jmr.2004.06.015

    Article  ADS  Google Scholar 

  • K. Nagayama P. Bachmann K. Wüthrich R.R. Ernst (1978) J. Magn. Reson. 31 133–148

    Google Scholar 

  • V.Y. Orekhov I.V. Ibraghimov M. Billeter (2001) J. Biomol. NMR 20 49–60 Occurrence Handle10.1023/A:1011234126930

    Article  Google Scholar 

  • J. Radon (1917) Berichte der Sächsischen Gesellschaft der Wissenschaften, Leipzig, Math-Phys. Kl. 69 262–277 Occurrence Handle46.0436

    MATH  Google Scholar 

  • P.N. Reardon L.D. Spicer (2005) J. Am. Chem. Soc. 127 10,848–10,849 Occurrence Handle10.1021/ja053145k

    Article  Google Scholar 

  • Rowland, S.W. (1979) In Image Reconstruction from Projections, Herman, G.T. (Ed.), Springer-Verlag, Berlin.

  • P. Schmieder A.S. Stern G. Wagner J.C. Hoch (1994) J. Biomol. NMR 4 483–490 Occurrence Handle10.1007/BF00156615

    Article  Google Scholar 

  • L.A. Shepp (1980) J. Comput. Assist. Tomogr. 4 94–107 Occurrence Handle81m:93084

    MathSciNet  Google Scholar 

  • Swarztrauber, P.N. (1982) In Parellel Computations, Rodrigue, G. (Ed.), Academic Press, New York

  • T. Szyperski G. Wider J.H. Bushweller K. Wuthrich (1993a) J. Biomol. NMR 3 127–132

    Google Scholar 

  • T. Szyperski G. Wider J.H. Bushweller K. Wuthrich (1993b) J. Am. Chem. Soc. 115 9307–9308 Occurrence Handle10.1021/ja00073a064

    Article  Google Scholar 

  • R.A. Venters B.E. Coggins D. Kojetin J. Cavanagh P. Zhou (2005) J. Am. Chem. Soc. 127 8785–8795 Occurrence Handle10.1021/ja0509580

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA

    Brian E. Coggins & Pei Zhou

Authors
  1. Brian E. Coggins
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pei Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pei Zhou.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Coggins, B.E., Zhou, P. PR-CALC: A Program for the Reconstruction of NMR Spectra from Projections. J Biomol NMR 34, 179–195 (2006). https://doi.org/10.1007/s10858-006-0020-z

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-006-0020-z

Keywords

Search

Navigation