CCP4 v4.2.2 Program References

Any publication arising from use of the CCP4 program suite should include the following reference:

Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763

abs

• Hao, Q. (2001), in preparation.

acorn

• Foadi,J., Woolfson,M.M., Dodson,E.J., Wilson,K.S., Yao Jia-xing and Zheng Chao-de (2000) Acta. Cryst. D56, 1137-1147.

almn

• R.A.Crowther, The Fast Rotation Function in The Molecular Replacement Method ed. M.G. Rossman, Int. Sci. Rev. Ser., no. 13, pp. 173-178 (1972).
• E.J.Dodson, in Molecular Replacement, Proceedings of the Daresbury Study Weekend, (1985) DL/SCI/R23

amore

• J.Navaza, Acta Cryst. A50, 157-163 (1994)
  (General reference.)
• J.Navaza. Acta Cryst. A43, 645-653 (1987)
  (Radial quadrature instead of bessel expansion)
• J.Navaza. Acta Cryst. A46, 619-620 (1990)
  (Stable recurrence relationship for rotation matrices.)
• G.A.Bentley, Some applications of the phased translation function using calculated phases in Molecular Replacement, Proceedings of the Daresbury Study Weekend, (1992) DL/SCI/R33
• E.E.Castellano et al., Fast Rigid-body Refinement for Molecular-replacement Techniques, J. Appl. Cryst. 25, 281-4 (1992).
• J.Navaza. Acta Cryst. D49, 588-591 (1993)
• Hirschfeld Acta Cryst. A24, 301-311 (1968)

anisoanl

• R.E.Rosenfield, K.N.Trueblood and J.D.Dunitz, Acta Cryst, A34, 828 - 829 (1978)
  Rigid-body postulate.
• T.R.Schneider, Proc. CCP4 Study Weekend, 133 - 144 (1996).
  Application of rigid-body postulate to protein SP445.
• V. Schomaker and K.N.Trueblood, Acta Cryst., B24, 63 - 76 (1968)
  Original description of TLS.
• V. Schomaker and K.N.Trueblood, Acta Cryst., B54, 507 - 514 (1998)
  Description of THMA program for small molecules, which fits TLS parameters (and more) to refined U values.

areaimol

• B.Lee and F.M.Richards, J.Mol.Biol., 55, 379 - 400 (1971)

beast

• R.J. Read (2001), "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57: 1373-1382.
  Click here to download.
• R.J. Read (1999), "Detecting outliers in non-redundant diffraction data." Acta Cryst. D55: 1759-1764.
• C. Chothia & A.M. Lesk (1986), "The relation between the divergence of sequence and structure in proteins." EMBO J. 5: 823-826.

cavenv

• A. Volbeda, private communication or with reference (in french): Anne Volbeda, Speleologie des hydrogenases a nickel et a fer. In: "Les Ecoles Physique et Chimie du Vivant, numero 1 - avril 1999, Analyse de l'organisation tridimensionnelle des proteines", pp 47-52.

crossec

• Don T. Cromer. `Calculation of Anomalous Scattering Factors at Arbitrary Wavelengths', J. Applied Cryst. 16 437-8 (1983)
• Cromer and Liberman. J. Chem. Phys. 53 1891-1898 (1970)
• Jensen. Physics Letters 74A 41-44 (1979)
• Cromer and Liberman Acta Cryst. A37 267-268 (1981)
• Henke, Gullikson and Davis, Atomic Data and Nuclear Data Tables Vol. 54 No.2 181-342 (1993).
  (See http://xray.uu.se/hypertext/henke.html)
  Note however that they are not given in fine intervals. This is only important in the immediate region of an absorption edge where they change quickly. In any case near edge features mean that any values of f' or f'' for an isolated atom in this region could be unreliable as they depend on the environment of the atom.
• Alain Soyer, J.Appl.Cryst. 28 244 (1995).
  The program Fhkl can plot values from the Henke et al and Cromer et al methods, though it is designed for other purposes.
• D. Waasmaier and A. Kirfel, `New Analytical Scattering Factor Functions for Free Atoms and Ions', Acta Cryst. A51 (1995).
  FTP Uni Wuerzburg

detwin

• Rees, D.C. Acta Cryst. (1980) A36, 578-581. The influence of Twinning by Merohedry on Intensity Statistics.
• Redinbo, M.R. and Yeates, T.O. (1993) Acta Cryst. D49, 375-380. Structure Determination of Plastocyanin from a Specimen with a Hemihedral Twinning Fraction of One-Half.
• Gomis-Ruth, F.X., Fita, I., Kiefersauer, R., Huber, R., Aviles, F.X. and Navaza, J. (1995) Acta Cryst D51, 819-823. Determination of Hemihedral Twinning and Initial Structural Analysis of Crystals of the Procarboxypeptidase A Ternary Complex.
• Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning.

distang

• IUPAC-IUB conventions, J. Mol. Biol., 50, 1 (1972).

dm

• K. Cowtan (1994), Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-38.
• Baker D., Bystroff C., Fletterick R., Agard D. (1994) Acta Cryst D49 429-439
• Bricogne, G. (1974) Acta Cryst A30 395-405
• Brunger, A. T. (1992) Nature 355, 472-474.
• Cowtan K. D., Main, P. (1993) Acta Cryst D49 148-157
• Sayre, D. (1974) Acta Cryst A30 180-184
• Schuller D. (1996) Acta Cryst D52 425-434
• Swanson, S. (1994) Acta Cryst D50 695-708
• Wang, B. C. (1985) Methods in Enzymology 115, 90-112
• Zhang, K. Y. J., Main P. (1990) Acta Cryst A46 377-381
• Abrahams, J. P. (1995) Acta Cryst D51 371-376
• K. D. Cowtan, P. Main (1996) Acta Cryst D52 43-48
• K. D. Cowtan (1999) in preparation.

dmmulti

K. Cowtan (1994), Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-38.

• Baker D., Bystroff C., Fletterick R., Agard D. (1994) Acta Cryst D49 429-439
• Bricogne, G. (1974) Acta Cryst A30 395-405
• Brunger, A. T. (1992) Nature 355, 472-474
• Cowtan K. D., Main, P. (1993) Acta Cryst D49 148-157
• Sayre, D. (1974) Acta Cryst A30 180-184
• Schuller D. (1996) Acta Cryst D52 425-434
• Swanson, S. (1994) Acta Cryst D50 695-708
• Wang, B. C. (1985) Methods in Enzymology 115, 90-112
• Zhang, K. Y. J., Main P. (1990) Acta Cryst A46 377-381

dyndom

• Method:
  S.Hayward, A.Kitao, H.J.C.Berendsen, Model-Free Methods of Analyzing Domain Motions in Proteins from Simulation: A Comparison of Normal Mode Analysis and Molecular Dynamics Simulation of Lysozyme Proteins, Structure, Function and Genetics, 27, 425, 1997.
• DynDom main reference:
  S.Hayward, H.J.C.Berendsen, Systematic Analysis of Domain Motions in Proteins from Conformational Change; New Results on Citrate Synthase and T4 Lysozyme Proteins, Structure, Function and Genetics, 30, 144, 1998.
• Applications:
  B.L.de Groot, S.Hayward, D.van Aalten, A.Amadei, H.J.C.Berendsen, Domain Motions in Bacteriophage T4 Lysozyme; a Comparison between Molecular Dynamics and Crystallographic Data Proteins, Structure, Function and Genetics, 31, 116, 1998.
  D.Roccatano, A.E.Mark,S.Hayward,Investigation of the Mechanism of Domain Closure in Citrate Synthase by Molecular Dynamics Simulation J. Mol. Biol. , 310, 1039, 2001.

fffear

• K. Cowtan (1998), Acta Cryst. D54, 750-756. Modified phased translation functions and their application to molecular fragment location.
• K. Cowtan (1998), Acta Cryst. D54, 750-756. Modified phased translation functions and their application to molecular fragment location.
• Kleywegt G. J., Jones T. A. (1997) Acta Cryst., D53, 179-185. Template convolution to enhance or detect structural features in macromolecular electron-density maps.
• Rossman M. G., Arnold E. (1993) International Tables for Crystallography Volume C, Section 2.3: Patterson and molecular replacement techniques (Kluwer Academic Publishers).

fffear fragment library

• K. Cowtan (2001), to be published.
• K. Cowtan (2001), to be published.
• H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P.E.Bourne (2000) Nucleic Acids Research 28, 235-242. The Protein Data Bank.
• L. Holm, C. Sander (1996) Science 273, 595-602. Mapping the protein universe.
• T. Oldfield (1992) J. Mol. Graphics 10, 247-252. SQUID - A program for the analysis and display of data from crystallography and molecular-dynamics.

ffjoin

• K. Cowtan (1998), Acta Cryst. D54, 750-756. Modified phased translation functions and their application to molecular fragment location.
• K. Cowtan (1998), Acta Cryst. D54, 750-756. Modified phased translation functions and their application to molecular fragment location.
• Kleywegt G. J., Jones T. A. (1997) Acta Cryst., D53, 179-185. Template convolution to enhance or detect structural features in macromolecular electron-density maps.

fft

• A.Immirzi, Crystallographic Computing Techniques, ed. F.R.Ahmed, Munksgaard, p399, (1966).
• L.F.Ten Eyck, Acta Cryst., A29, 486, (1973).
• R.J.Read and A.J.Schierbeek J. Appl. Cryst. 21 490-495 (1988).

fhscal

• Kraut J, Sieker LC, High DF and Freer ST, Proc. Nat. Acad. Sci. USA, 48, 1417-1424 (1962).

findncs

• Lu,G. (1999) FINDNCS: A program to detect non-crystallographic symmetries in protein crystals from heavy atoms sites J. Appl. Cryst. 32 365

freerflag

• A.T. Brünger, Nature 355, 472-4 (1992)
• A.T. Brünger, "Free R Value: Cross-validation in crystallography", Methods in Enzym. 277, 366-396 (1997).
  See The Brunger Lab Publications for more references on the Free R.

getax

• C. Vonrhein and G. E. Schulz, Acta Cryst., D55, 225 - 229 (1999)
  Locating proper non-crystallographic symmetry in low-resolution electron-density maps with the program GETAX.

lsqkab

• Kabsch W. Acta. Cryst. A32 922-923 (1976).

maprot

• Stein et al., Structure 2, 45-47 (1994)

matthews_coef

• Matthews, J.Mol.Biol 33, 491-497 (1968).

oasis

• Hao, Q.*, Gu, Y.X., Zheng, C.D. & Fan, H.F. (2000) J. Appl. Cryst. 33, 980-981. "OASIS: A Program for Breaking Phase Ambiguity in OAS or SIR".
• Fan, H. F. and Gu, Y. X. (1985) Combining direct methods with isomorphous replacement or anomalous scattering data III. The incorporation of partial structure information, Acta Cryst. A41, 280-284.
• Fan H. F., Hao, Q., Gu, Y. X., Qian, J. Z., Zheng, C. D. and Ke, H. (1990) Combining direct methods with isomorphous replacement or anomalous scattering data VII. Ab initio phasing of the OAS data from a small protein, Acta Cryst. A46, 935-939.
• Y. -D. Liu, I. Harvey, Y. -X. Gu, C. -D. Zheng, Y. -Z. He, H. -F. Fan, S. S. Hasnain and Q. Hao (1999) Is single-wavelength anomalous scattering sufficient for solving phases? A comparison of different methods for a 2.1 A structure solution, Acta Cryst. D55, 1620-1622.

omit

• T.N. Bhat, "CALCULATION OF AN OMIT MAP", J. Appl. Cryst., 21, 279-281 (1988)
• F.M.D.Vellieux and B.W.Dijkstra, "Computation of Bhat's OMIT maps with different coefficients", J. Appl. Cryst., 30, 396-399 (1997)

overlapmap

• Branden C. and Jones A., Nature 343 687-689 (1990)
• Jones Y. and Stuart D, Proc. of CCP4 Study Weekend on Isomorphous Replacement And Anomalous Scattering, 1991 39-48.

polypose

• R. Diamond, Protein Science, 1, 1279-1287 (1992)

postref

• Winkler F.K., Schutt C.E. & Harrison S.C., Acta Cryst., (1979), A35, 901 - 911.
• Greenhough T.J. & Helliwell J.R., J. Appl. Cryst., (1982), 15, 493 - 508
• Greenhough T.J., CCP4 Information Quarterly for Protein Crystallography, Feb. 1983, Daresbury Laboratory.

protin

• Refinement of Protein Structures (Proceedings of the Daresbury Study Weekend, SERC Daresbury Laboratory, 1980) Compiled by P.A. Machin, J.W. Campbell and M. Elder.
• Macromolecular Refinement (Proceedings of the CCP4 Study Weekend, 1996), ed. E. Dodson, M. Moore, A. Ralph and S. Bailey.

rantan

• Yao Jia-xing, (1981). Acta. Cryst. A37, 642-644.
• Germain,G. and Woolfson,M.M. (1968) Acta. Cryst. B24, 91-97.
• Karle,J. and Hauptman,H. (1956) Acta. Cryst. 9, 635.
• Yao Jia-xing, (1983). Acta. Cryst. A39, 35-37.

refmac

• "Application of Maximum Likelihood Refinement" G. Murshudov, A.Vagin and E.Dodson, (1996) in the Refinement of Protein structures, Proceedings of Daresbury Study Weekend.
• "Refinement of Macromolecular Structures by the Maximum-Likelihood Method" G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) in Acta Cryst. D53, 240-255
• "Efficient anisotropic refinement of Macromolecular structures using FFT" G.N.Murshudov, A.Lebedev, A.A.Vagin, K.S.Wilson and E.J.Dodson (1999) Acta Cryst. section D55, 247-255

restrain

• Cruickshank D W J (1965) Computing Methods in Crystallography, (J S Rollett, ed.), pp. 112-116, Oxford, Pergamon Press.
• Driessen H, Haneef M I J, Harris G W, Howlin B, Khan G and Moss D S (1989) J Appl Cryst., 22, 510-516.
• Engh R A and Huber R (1991) Acta Cryst. A, -.
• Haneef I, Moss D S, Stanford M J and Borkakoti N (1985) Acta Cryst., A41, 426-433.
• Howlin B, Butler S A, Moss D S, Harris G W and Driessen H P C (1993) J. Appl. Crystallogr. 26, 622-624.
• Johnson C K and Levy M A (1974) in International Tables for X-ray Crystallography, Vol IV (Ibers, J.A. and Hamilton, W.C., eds.), pp. 320-332.
• Jones T A, Zou J Y, Cowan S W and Kjeldgaard M (1991) Acta Cryst., A47, 110-119.
• Moss D S (1981) Refinement of protein structures, Proceedings of the Daresbury Study Weekend, (P Machin, ed.), pp. 9-12, Daresbury, SERC.
• Moss D S & Morffew A J (1982) Comput Chem, 6, 1-3.
• Nielsen K (1977) Acta Cryst., A33, 1009-1010.
• Rees B (1976) Acta Cryst., A32, 483-488.
• Rollett J S (1965) Computing Methods in Crystallography, pp. 38-56. Oxford, Pergamon Press.
• Waser J (1963) Acta Cryst., 16, 1091-1094.

revise

• Fan Hai-fu, Woolfson, M.M. & Yao Jia-xing, (1993). Proc. R. Soc. Lond. A 442, 13-32.

rotamer

• Lovell, S.C., Word, J.M., Richardson, J.S. & Richardson, D.C. "The penultimate rotamer library", Proteins: Structure, Function and Genetics, Vol.40, 389-408 (2000).
• Hooft, R.W.W., Vriend, G., Sander, C. & Abola, E.E. "Errors in protein structures", Nature, Vol. 381, 272 (1996).

rsps

• Knight, S.D. (2000): RSPS version 4.0: a semi-interactive vector-search program for solving heavy-atom derivatives, Acta Cryst. D 52, 42-47
• Knight, S.D. (1989): Ribulose 1,5-Bisphosphate Carboxylase/ Oxygenase - A Structural Study, Thesis, Swedish University of Agricultural Sciences, Uppsala.
• Blundell, T.L. & Johnson, L.N. (1976). "Protein Crystallography", Academic Press, London.
• Stout, G.H. & Jensen, L.H. (1989). "X-Ray Structure Determination. A Practical Guide", 2nd edition, John Wiley & Sons, New York.

sapi

• Hao, Gu, Yao, Zheng & Fan (2001) in preparation.

sc

• Michael C. Lawrence and Peter M. Colman J. Mol. Biol., 234, p946 - p50 (1993)
• M. L. Connolly J. Appl. Crystallogr., 16, p548 - p558 (1983)
• F. M. Richards Annu. Rev. Biophys. Bioeng, 6, p151-176 (1977)
• A.J. Nicholls Biophys. J., 64, A116 (1993)

scala

• W. Kabsch, J.Appl.Cryst. 21, 916-924 (1988)
• P.R.Evans, "Data reduction", Proceedings of CCP4 Study Weekend, 1993, on Data Collection & Processing, pages 114-122
• P.R.Evans, "Scaling of MAD Data", Proceedings of CCP4 Study Weekend, 1997, on Recent Advances in Phasing, Click here
• R.Read, "Outlier rejection", Proceedings of CCP4 Study Weekend, 1999, on Data Collection & Processing
• Hamilton, Rollett & Sparks, Acta Cryst. 18, 129-130 (1965)
• Blessing, R.H., Acta Cryst. A51, 33-38 (1995)
• Kay Diederichs & P. Andrew Karplus,"Improved R-factors for diffraction data analysis in macromolecular crystallography", Nature Structural Biology, 4, 269-275 (1997)
• Manfred Weiss & Rolf Hilgenfeld, "On the use of the merging R factor as a quality indicator for X-ray data", J.Appl.Cryst. 30, 203-205 (1997)
• Manfred Weiss, "Global Indicators of X-ray data quality" J.Appl.Cryst. 34, 130-135 (2001)

scaleit

• Normal Probability Analysis:
  Lynne Howell and Dave Smith, J.Appl. Cryst. 25 81-86 (1992)

sfall

• Agarwal, R.C., Acta Cryst., (1978), A34, 791-809.
• International Tables for X-ray Crystallography, Vol.IV, (1974), Kynoch Press.
• Ten Eyck, L.F., Acta Cryst., (1977), A33, 486.
• Bruenger, A.T., Nature 355, 472-4 (1992)
• International Tables for Crystallography, vol. C, (1995), Kluwer.
• "Refinement of protein structures", Proceedings of the Daresbury Study Weekend 15-16 November, 1980 (Compiled by P.S. Machin, J.W. Campbell and M. Elder).

sftools

• B. Hazes, unpublished results

sigmaa

• Read, R.J.: Acta Cryst. A42 (1986) 140-149.
• Srinivasan, R.: Acta Cryst. 20 (1966) 143-144.
• Hauptman, H.: Acta Cryst. A38 (1982) 289-294.
• Luzzati, V.: Acta Cryst. 6 (1953) 142-152.
• Rogers, D. in Computing Methods in Crystallography (Rollett, J.S.,ed.) (1985) pp. 126-127, Pergamon Press.
• Hendrickson, W.A. & Lattman, E.E.: Acta Cryst. B26 (1970) 136-143.
• Bricogne, G.: Acta Cryst. A32 (1976) 832-847.
• Sim, G.A.: Acta Cryst. 12 (1959) 813-815; 13 (1960) 511-512.
• Read, R. J.: Acta Cryst. A46 (1990) 140-9.
• Read, R. J.: Acta Cryst. A46 (1990) 900-12.
• Vellieux, F.M.D., Livnah, O., Dym, O., Read, R.J. & Sussman, J.L., manuscript in preparation.

solomon

• Abrahams J. P. and Leslie A. G. W., Acta Cryst. D52, 30-42 (1996)

surface

• B.Lee and F.M.Richards, J.Mol.Biol., 55, 379 - 400 (1971)
• Chothia (1975), "Structural Invariants in Protein Folding", Nature 254: 304-308

tffc

• Molecular Replacement, Proceedings of the Daresbury Study Weekend, (1985) DL/SCI/R23
• Molecular Replacement, Proceedings of the Daresbury Study Weekend, (1992) DL/SCI/R33

tlsanl

• B.Howlin, S.A.Butler, D.S.Moss, G.W.Harris and H.P.C.Driessen, "TLSANL: TLS parameter analysis program for segmented anisotropic refinement of macromolecular structures.", J. Appl. Cryst., 26, 622-624 (1993)
• V.Schomaker and K.N.Trueblood Acta Cryst., B24, 63 (1968)

topp

• Lu G., A WWW service system for automatic comparison of protein structures Protein Data Bank Quarterly Newsletter, #78, 10-11. 1996
• Guoguang Lu, An automatic topological and atomic comparison program for protein structures (in manuscript or http://gamma.mbb.ki.se/~guoguang/top.html).

truncate

• French G.S. and Wilson K.S. Acta. Cryst. (1978), A34 , 517.

vecref

• Busing WR and Levy HA (1961) in Computing Methods and the Phase Problem in X-ray Crystal Analysis, Pergamon, Oxford.
• Kraut J, Sieker LC, High DF, Freer ST (1962), Proc. Nat. Acad. Sci. USA, 48, 1417-1424.

xdldataman

• XDLDATAMAN:
  G.J. Kleywegt & T.A. Jones (1996), Acta Cryst. D52, 826-828.
• XDL_VIEW:
  J.W. Campbell (1995). "XDL_VIEW, an X-windows-based toolkit for crystallographic and other applications", J. Appl. Cryst. 28, 236-242.
• RAVE:
  G.J. Kleywegt & T.A. Jones (1994). "Halloween ... Masks and Bones", in "From First Map to Final Model" (S. Bailey, R. Hubbard & D. Waller, Eds.), SERC Daresbury Laboratory, pp. 59-66.
• O:
  T.A. Jones, J.Y. Zou, S.W. Cowan, & M. Kjeldgaard (1991). "Improved methods for building protein models in electron density maps and the location of errors in these models", Acta Cryst. A47, 110-119.
• GEMINI:
  E. Stanley (1972). "The identification of twins from intensity statistics", J. Appl. Cryst. 5, 191-194.
• GEMINI:
  D.C. Rees (1980). "The influence of twinning by merohedry on intensity statistics", Acta Cryst. A36, 578-581.
• RFREE:
  A.T. Brunger (1992). "Free R value: a novel statistical quantity for assessing the accuracy of crystal structures", Nature 355, 472-475.
• CCP4:
  Collaborative Computational Project Number 4 (1994). "The CCP4 suite: programs for protein crystallography", Acta Cryst. D50, 760-763.

xdlmapman

• XDLMAPMAN:
  G.J. Kleywegt & T.A. Jones (1996), Acta Cryst. D52, 826-828.
• XDL_VIEW:
  J.W. Campbell (1995). "XDL_VIEW, an X-windows-based toolkit for crystallographic and other applications", J. Appl. Cryst. 28, 236-242.
• RAVE:
  G.J. Kleywegt & T.A. Jones (1994). "Halloween ... Masks and Bones", in "From First Map to Final Model" (S. Bailey, R. Hubbard & D. Waller, Eds.), SERC Daresbury Laboratory, pp. 59-66.
• MINI-MAPS:
  T.A. Jones (1978). "A graphics model building and refinement system for macromolecules", J. Appl. Cryst. 11, 268-272.
• O/BONES:
  T.A. Jones, J.Y. Zou, S.W. Cowan, & M. Kjeldgaard (1991). "Improved methods for building protein models in electron density maps and the location of errors in these models", Acta Cryst. A47, 110-119.
• SKELETONISATION:
  J. Greer (1974). "Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins", J. Mol. Biol. 82, 279-301.
• PEAK-PICKING:
  G.J. Kleywegt, G.W. Vuister, A. Padilla, R.M.A. Knegtel, R. Boelens, & R. Kaptein (1993). "Computer-assisted assignment of homonuclear 3D NMR spectra of proteins. Application to pike parvalbumin III", J. Magn. Reson. B102, 166-176.
• CCP4:
  Collaborative Computational Project Number 4 (1994). "The CCP4 suite: programs for protein crystallography", Acta Cryst. D50, 760-763.