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Advanced Applications of Shelxd and Shelxe

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Advancing Methods for Biomolecular Crystallography
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Abstract

The programs shelxc, shelxd, and shelxe by G. Sheldrick provide a powerful pipeline for experimental phasing of various phasing scenarios, like MAD, SIRAS, or MR-SAD. They are command line programs, which is the reason why many people are discourage from using them and exploiting their power. This tutorial shows that shelx c/d/e are not very difficult to use and only little knowledge is required to solve the phase problem and create and initial poly-Alanine model and an interpretable map with very little effort.

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Notes

  1. 1.

    NB: this was before the auto-tracing capabilities of shelxe by which the effect of recycling the substructure has become less important.

  2. 2.

    β-versions of the shelx-Programs are available to registered shelx-users upon email request to either George Sheldrick or me. Registration is free of charge for academics and only requires the sending of a fax to the institute. See http://shelx.uni-ac.gwdg.de for details.

References

  1. Bricogne G, Vonrhein C, Flensburg C, Schiltz M, Paciorek W (2003) Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr D Biol Crystallogr 59:2023–2030

    Article  CAS  Google Scholar 

  2. Caliandro R, Carrozzini B, Cascarano GL, De Caro L, Giacovazzo C, Siliqi D (2005) Ab initio phasing at resolution higher than experimental resolution. Acta Crystallogr D Biol Crystallogr 61:1080–1087

    Article  Google Scholar 

  3. Carter CW Jr, Sweet RM (eds) (1997) Macromolecular crystallography, vol 276(A), Methods in enzymology. Academic Press, New York, pp 307–326

    Google Scholar 

  4. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760–763

    Article  Google Scholar 

  5. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D D Biol Crystallogr 66:486–501

    Article  CAS  Google Scholar 

  6. Jia-xing Y, Woolfson MM, Wilson KS, Dodson EJ (2005) A modified ACORN to solve protein structures at resolutions of 1. 7 Å or better. Acta Crystallogr D Biol Crystallogr 61:1465–1475

    Article  Google Scholar 

  7. Kabsch W (2010) XDS. Acta Crystallogr Biol Crystallogr 66:125–132

    Article  Google Scholar 

  8. Morris RJ, Perrakis A, Lamzin V (2002) ARP/wARP’s model – building algorithms. I. The main chain. Acta Crystallogr D Biol Crystallogr 58:968–975

    Article  Google Scholar 

  9. Nanao MH, Sheldrick GM, Ravelli RBG (2005) Improving radiation-damage substructures for RIP. Acta Crystallogr D Biol Crystallogr 61:1227–1237

    Article  Google Scholar 

  10. Ness SR, de Graff RAG, Abrahams JP, Pannu NS (2004) CRANK: new methods for automated macromolecular crystal structure solution. Structure 12:1753–1761

    Article  CAS  Google Scholar 

  11. Panjikar S et al (2005) Auto-Rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment. Acta Crystallogr D Biol Crystallogr 61:449–457

    Article  Google Scholar 

  12. Panjikar S et al (2009) On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination. Acta Crystallogr D Biol Crystallogr 65:1089–1097

    Article  Google Scholar 

  13. Pape T, Schneider TR (2004) HKL2MAP: a graphical user interface for phasing with SHELX programs. J Appl Cryst 37:843–844

    Article  CAS  Google Scholar 

  14. Ravelli RBG, Nanao MH, Lovering A, White S, McSweeney S (2005) Phasing in the presence of radiation damage. J Synchrotron Radiat 12:276–284

    Article  CAS  Google Scholar 

  15. Rodríguez DD et al (2009) Crystallographic ab initio protein structure solution below atomic resolution. Nat Methods 6(9):651–653

    Article  Google Scholar 

  16. Rudiño-Piñera E et al (2007) The solution and crystal structures of a module pair from the staphylococcus aureus-binding site of human fibronectin-a tale with a twist. J Mol Biol 368:833–844

    Article  Google Scholar 

  17. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122 G.M. Sheldrick,

    Google Scholar 

  18. Sheldrick GM (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D Biol Crystallogr 66:479–485

    Article  Google Scholar 

  19. Thorn A, Sheldrick GM (2011) ANODE: anomalous and heavy-atom density calculation. J Appl Cryst 44:1285–1287

    Article  CAS  Google Scholar 

  20. UsĂ³n I, Stevenson CEM, Lawson DM, Sheldrick GM (2007) Structure determination of the O-methyltransferase NovP using the ’free lunch algorithm’ as implemented in SHELXE. Acta Crystallogr D Biol Crystallogr 63:1069–1074

    Article  Google Scholar 

  21. Vonrhein C, Blanc E, Roversi P, Bricogne G (2007) Automated structure solution with autoSHARP. Methods Mol Biol 364:215–230

    CAS  Google Scholar 

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Acknowledgements

Discussions with and presentations from G. Sheldrick are the main source of information for this document. Some parts of this document were copied verbatim from his presentations with permission.

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Correspondence to Tim GrĂ¼ne .

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GrĂ¼ne, T. (2013). Advanced Applications of Shelxd and Shelxe. In: Read, R., Urzhumtsev, A., Lunin, V. (eds) Advancing Methods for Biomolecular Crystallography. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6232-9_15

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