CCP4 v6.5 Program References

Any publication arising from use of the CCP4 software suite should include both references to the specific programs used (see below) and the following reference to the CCP4 suite:

M. D. Winn et al. Acta. Cryst. D67, 235-242 (2011)
"Overview of the CCP4 suite and current developments"
[ doi:10.1107/S0907444910045749 ]

Such citations are vital to the CCP4 project, and individual program authors, in maintaining funding and thus being able to develop CCP4 further.

The following list is meant as an aid to citation of individual programs, but is not complete. It has been extracted from the individual program documentation, so look there for more details. In addition, many relevant articles can be found in the proceedings of the 2010 Study Weekend, published as a special issue of Acta Cryst D.

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.
• "Incorporation of Prior Phase Information Strengthen Maximum-Likelihood Structure Refinemen" N.J.Pannu, G.N.Murshudov, E.J.Dodson and R.J.ReadA (1998) Acta Cryst. section D54, 1285-1294.
• "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.
• "Use of TLS parameters to model anisotropic displacements in macromolecular refinement" M. Winn, M. Isupov and G.N.Murshudov (2000) Acta Cryst. 2001:D57 122-133
• "Fisher's information matrix in maximum likelihood molecular refinement." Steiner R, Lebedev, A, Murshudov GN. Acta Cryst. 2003 D59: 2114-2124
• "Macromolecular TLS refinement in REFMAC at moderate resolutions," Winn MD, Murshudov GN, Papiz MZ. Method in Enzymology, 2003:374 300-321
• "Direct incorporation of experimental phase information in model refinement" Skubak P, Murshudov GN, Pannu NS. Acta Cryst. 2004 D60: 2196-2201
• "REFMAC5 dictionary: organisation of prior chemical knowledge and guidelines for its use." Vagin, AA, Steiner, RS, Lebedev, AA, Potterton, L, McNicholas, S, Long, F and Murshudov, GN. Acta Cryst. 2004 D60: 2284-2295

abs

• Hao, Q. (2004) J. Appl. Cryst. 37, 498-499. ABS: a program to determine absolute configuration and evaluate anomalous scatterer substructure.

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.
• Yao Jia-xing (2002) Acta. Cryst. D58, 1941-1947.
• Yao Jia-xing, Woolfson,M.M., Wilson,K.S. and Dodson,E.J. (2002) Z. Kristallogr. 217, 636-643.
• Yao Jia-xing, Woolfson,M.M., Wilson,K.S. and Dodson,E.J. (2005) Acta. Cryst. D61, 1465-1475.

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)
• F.L.Hirshfeld Acta Cryst. A24, 301-311 (1968)

anisoanl

• Martyn Winn, CCP4 Newsletter March 2001, 39
  ANISOANL - analysing anisotropic displacement parameters
• 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)
• E.B.Saff and A.B.J.Kuijlaars, The Mathematical Intelligencer, 19, 5-11 (1997)
  http://www.math.vanderbilt.edu/~esaff/texts/161.pdf

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. Click here to download.
• C. Chothia & A.M. Lesk (1986), "The relation between the divergence of sequence and structure in proteins." EMBO J. 5: 823-826.

bulk

• A. Fokine, G. Capitani, M.G. Grutter, A. Urzhumtsev, J. Appl. Cryst. 36 352-355 (2003)
• A. Fokine and A. Urzhumtsev, Acta Cryst. A58 72-74 (2002)
• A. Fokine and A. Urzhumtsev, Acta Cryst. D58 1387-1392 (2002)

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.

ccp4i

• Elizabeth Potterton, Peter Briggs, Maria Turkenburg and Eleanor Dodson (2003) Acta. Cryst. D59 1131-1137 "A graphical user interface to the CCP4 program suite"

chainsaw

• N. Stein, J. Appl. Cryst. 41, 641 - 643 (2008).
  CHAINSAW: a program for mutating pdb files used as templates in molecular replacement.
• R. Schwarzenbacher et al., Acta Cryst. D60, 1229 - 1236 (2004).
  The importance of alignment accuracy for molecular replacement.

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

ctruncate

• S. French and K. Wilson, Acta Cryst. A34, 517-525 (1978).
• T. O. Yeates, Acta Cryst. A44, 142-144 (1980).
• J. E. Padilla and T. O. Yeates, Acta Cryst. D59, 1124-1130 (2003).
• P. Zwartz, CCP4 Newsletter 42.
• Z. Dauter, Acta Cryst. D62, 867 (2006)
• P. Zwartz, Acta Cryst. D61, 1437 (2006)

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.
• Murray-Rust, P. (1973) Acta Cryst B29, 2559-2566.

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) Acta Cryst D55 1555-1567

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), Fast Fourier feature recognition, Acta Cryst. D57, 1435-1444.
• 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, 183, (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-atom 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.

fsearch

• Hao, Q. (2001), Acta Cryst. D57 1410-1414. "Phasing from an Envelope".
• Q. Liu, A. J. Weaver, T. Xiang, D. J. Thiel and Q. Hao, (2003) Acta Cryst. D59 1016-1019. "Low-resolution molecular replacement using a six-dimensional search"

gesamt

• E.Krissinel (2012), Enhanced Fold Recognition using Efficient Short Fragment Clustering, in preparation

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).
• Kantardjieff and Rupp, Protein Science 12, 1865-1871 (2003).

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.

pdb_extract

• Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
  H. Yang, V. Guranovic, S. Dutta, Z. Feng, H. M. Berman and J. D. Westbrook Acta Cryst. D60, 1833-1839 (2004)

phaser-2.5.0

Citation:

J. Appl. Cryst. (2007). 40, 658-674. Phaser crystallographic software. A. J. McCoy, R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L.C. Storoni and R.J. Read.

Other references:

1. Read, R.J. (2001). Pushing the boundaries of molecular replacement with maximum likelihood. Acta Cryst. D57, 1373-1382
2. Storoni, L.C., McCoy, A.J. & Read, R.J. (2004). Likelihood-enhanced fast rotation functions. Acta Cryst D60, 432-438
3. McCoy, A.J., Grosse-Kunstleve, R.W., Storoni, L.C. & Read, R.J. (2005). Likelihood-enhanced fast translation functions. Acta Cryst D61, 458-464
4. McCoy, A.J., Storoni, L.C. and Read, R.J. (2004) Simple algorithm for a maximum-likelihood SAD function Acta Cryst. D60, 1220-1228.
   

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.

r500

• Clowney et al., J. Am. Chem. Soc. 118, 509-518 (1996)
  (Geometric Parameters in Nucleic Acids: Nitrogenous Bases.)
• Engh, R.A. & Huber, R. International Tables for Crystallography (Vol. F). 18.3, 382-392 (2006)
  (Structure quality and target parameters.)
• M. Jaskolski, M. Gilski, Z. Dauter & A. Wlodawer Acta Cryst. D63 611-620 (2007)
  (Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?)
• Kleywegt, G.G. & Jones, T.A. Structure 4, 1395-1400 (1996)
  (Phi/Psi-chology: Ramachandran revisited. )

rampage

• S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, D.C. Richardson, Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Struct. Funct. Genet. 50 437-450 (2003).

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.

rapper

• P.I.W. de Bakker, M.A. DePristo, D.F. Burke, T.L. Blundell (2002) Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins Struct. Funct. Genet. 51 21-40.

• S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, D.C. Richardson (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Struct. Funct. Genet. 50 437-450.

• M.A. DePristo, P.I.W. de Bakker, S.C. Lovell, T.L. Blundell (2002) Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles. Proteins Struct. Funct. Genet. 51 41-55.

• M.A. DePristo, P.I.W. de Bakker, R.P. Shetty, T.L. Blundell (2003) Discrete restraint-based protein modeling and the Cα-trace problem. Protein Science 12 2032-2046.

• R.P. Shetty, P.I.W. de Bakker, M.A. DePristo, T.L. Blundell (2003) The advantages of fine-grained side chain conformer libraries. Protein Engineering 16 963-969.

• M.A. DePristo, P.I.W. de Bakker, T.L. Blundell (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure (Camb.) 12 831-838.

• M.A. Depristo, P.I.W. de Bakker, R.J. Johnson, T. L. Blundell. (2005) Crystallographic refinement by knowledge-based exploration of complex energy landscapes. Structure 13 (9) 1311-1319.

• N. Furnham, T. L. Blundell, M.A. Depristo, T. C. Terwilliger. (2006) Is one Solution Good Enough? Nature Structural & Molecular Biology 13 (3) 184-185.

• N. Furnham, Andrew S. Dore, Dimitri Y. Chirgadze, Paul I. W. de Bakker, M.A. Depristo, T. L. Blundell. (2006) Knowledge-Based Real-Space Explorations for Low-Resolution Structure Determination Structure 14 (8) 1313-1320.

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. A47, 392-400.
• 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

• Q. Hao, Y. X. Gu, J. X. Yao, C. D. Zheng and H. F. Fan (2003) J. Appl. Cryst. 36 1274-1276. "SAPI: a direct-methods program for finding heavy-atom sites with SAD or SIR data."

sc

• Michael C. Lawrence and Peter M. Colman J. Mol. Biol., 234, p946 - p950 (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)

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)

superpose

• E.Krissinel and K.Henrick (2004), Acta Cryst. D60, 2256-2268 Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

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)
• E.A.Merritt Acta Cryst., D55, 1997 (1999)

topdraw

• Bond, C.S. (2003) Bioinformatics 19, 311-2.

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.