2012
-
Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV,
Grosse-Kunstleve RW, Hung L-W:
Improved crystallographic models through iterated local
density-guided model deformation and reciprocal-space refinement
Acta Cryst. 2012, D68, 861-870.
(Reprint)
-
Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H,
Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B,
Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA,
DiFiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM,
Sokaras D, Weng T-C, Zwart PH, White WE, Adams PD, Bogan MJ,
Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U,
Yano J, Yachandra VK:
Room temperature femtosecond X-ray diffraction of
photosystem II microcrystals
PNAS 2012, June 4, published ahead of print.
[doi:10.1073/pnas.1204598109]
-
Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams PD:
Automatic Fortran to C++ conversion with FABLE
Source Code for Biology and Medicine 2012, 7:5.
[doi:10.1186/1751-0473-7-5]
-
Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkoczi G, Chen VB, Headd
JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS,
Terwilliger TC, Adams PD:
Graphical tools for macromolecular crystallography in PHENIX
J. Appl. Cryst. 2012, 45, 581-586.
(Reprint)
-
Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty
NW, Richardson DC, Richardson JS, Adams PD:
Use of knowledge-based restraints in phenix.refine to improve
macromolecular refinement at low resolution
Acta Cryst. 2012, D68, 381-390.
(Reprint)
-
Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD:
Towards automated crystallographic structure refinement with
phenix.refine
Acta Cryst. 2012, D68, 352-367.
(Reprint)
- Liu HG, Poon BK, Chen G, Grosse-Kunstleve RW, Zwart PH:
CCTBX tools for derivative-free optimization
Computational Crystallography Newsletter 2012, 3, 22-27.
(Reprint)
2011
- Brunger AT, Adams PD, DeLano WL, Gros P, Grosse-Kunstleve RW,
Jiang JS, Pannu NS, Read RJ, Rice LM, Simonson T:
CNS, a program system for structure-determination and refinement
In International Tables for Crystallography, Volume F:
Crystallography of biological macromolecules,
M.G. Rossmann, D.M. Himmel and E. Arnold, Eds., 2nd edition,
John Wiley & Sons, 2011, 512-519.
- Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N,
Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ,
Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS,
Terwilliger TC, Zwart PH:
PHENIX: a comprehensive Python-based system for macromolecular
structure solution
In International Tables for Crystallography, Volume F:
Crystallography of biological macromolecules,
M.G. Rossmann, D.M. Himmel and E. Arnold, Eds., 2nd edition,
John Wiley & Sons, 2011, 539-547.
- Gildea RJ, Bourhis LJ, Dolomanov OV, Grosse-Kunstleve RW, Puschmann H,
Adams PD, Howard JAK:
iotbx.cif: a comprehensive CIF toolbox
J. Appl. Cryst. 2011, 44, 1259-1263.
(Reprint)
- Adams PD, Afonine PV, Bunkoczi G, Chen VB, Echols N, Headd JJ,
Hung L-W, Jain S, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ,
Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS,
Terwilliger TC, Zwart PH:
The Phenix software for automated determination of macromolecular
structures
Methods 2011, 55:94-106.
- Afonine PV, Echols N, Grosse-Kunstleve RW, Moriarty NW, Adams PD:
Improved target weight optimization in phenix.refine
Computational Crystallography Newsletter 2011, 2, 99-103.
(Reprint)
- Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams PD:
Exact direct-space asymmetric units for the 230 crystallographic
space groups
Acta Cryst. 2011, A67, 269-275.
(Reprint)
- Grosse-Kunstleve RW, Echols N, Adams PD:
Fuzzy space group symbols: H3 and H32
Computational Crystallography Newsletter 2011, 2, 12-14.
(Reprint)
- Grosse-Kunstleve RW, Bourhis LJ:
Electron density illustrations
Computational Crystallography Newsletter 2011, 2, 25-28.
(Reprint)
2010
- Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW,
Langan P, Adams PD:
Joint X-ray and neutron refinement with phenix.refine
Acta Cryst. 2010, D66, 1153-1163.
(Reprint)
- Grosse-Kunstleve RW, Adams PD:
cctbx PDB handling tools
Computational Crystallography Newsletter 2010, 1, 4-11.
(Reprint)
- Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW,
Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD:
phenix.model_vs_data: a high-level tool for the calculation of
crystallographic model and data statistics
J. Appl. Cryst. 2010, 43, 669-676.
(Reprint)
- Poon BK, Grosse-Kunstleve RW, Zwart PH & Sauter NK:
Detection and correction of underassigned rotational symmetry
prior to structure deposition
Acta Cryst. 2010, D66, 503-513.
(Reprint)
- Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N,
Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ,
Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS,
Terwilliger TC, Zwart PH:
PHENIX: a comprehensive Python-based system for macromolecular
structure solution
Acta Cryst. 2010, D66, 213-221.
(Reprint)
2009
- Grosse-Kunstleve RW, Terwilliger TC, Adams PD:
Experience converting a large Fortran-77 program to C++
Newsletter of the IUCr Commission on Crystallographic Computing 2009, 10, 75-84.
(Reprint)
- Grosse-Kunstleve RW, Moriarty NW, Adams PD:
Torsion Angle Refinement and Dynamics as a Tool to Aid
Crystallographic Structure Determination
Proceedings of ASME 2009 International Design Engineering Technical
Conferences, San Diego, California,
August 30 - September 2, 2009,
Paper #DETC2009-87737, ASME Press.
(Reprint)
- Moriarty NW, Grosse-Kunstleve RW, Adams PD:
electronic Ligand Builder and Optimization Workbench (eLBOW):
a tool for ligand coordinate and restraint generation
Acta Cryst. 2009, D65, 1074-1080.
(Reprint)
- Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS,
Richardson DC, Terwilliger TC:
Recent developments in phasing and structure refinement for
macromolecular crystallography
Current Opinion in Structural Biology 2009, 19, 566-572.
- Afonine PV, Grosse-Kunstleve RW, Urzhumtsev A, Adams PD:
Automatic multiple-zone rigid-body refinement with a large
convergence radius.
J. Appl. Cryst. 2009, 42, 607-615.
(Reprint)
- Terwilliger TC, Adams PD, Read RJ, Mccoy AJ, Moriarty NW,
Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung L-W:
Decision-making in structure solution using Bayesian estimates of
map quality: the PHENIX AutoSol wizard.
Acta Cryst. 2009, D65, 582-601.
(Reprint)
-
Elomari S, Burton A, Medrud RC, Grosse-Kunstleve RW:
The synthesis, characterization, and structure solution of SSZ-56:
An extreme example of isomer specificity in the structure direction
of zeolites.
Microporous and Mesoporous Materials 2009, 118, 325-333.
2008
- Terwilliger TC, Grosse-Kunstleve RW, Afonine PV,
Moriarty NW, Zwart P, Hung L-W, Read RJ, Adams PD:
Iterative model building, structure refinement and density
modification with the PHENIX AutoBuild wizard
Acta Cryst. 2008, D64, 61-69.
(Reprint)
- Zwart P, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD:
Surprises and pitfalls arising from(pseudo)symmetry
Acta Cryst. 2008, D64, 99-107.
(Reprint)
- Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW,
Adams PD, Read RJ, Zwart PH, Hung L-W:
Iterative-build OMIT maps: map improvement by iterative model building
and refinement without model bias.
Acta Cryst. 2008, D64, 515-524.
(Reprint)
- Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung L-W, Ioerger TR,
McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK,
Storoni LC, Terwilliger TC, Adams PD:
Automated Structure Solution with the PHENIX Suite.
Methods in Molecular Biology 2008, 426, 419-436.
2007
- Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD,
Moriarty NW, Zwart P, Read RJ, Turk D, Hung L-W:
Interpretation of ensembles created by multiple iterative rebuilding
of macromolecular models.
Acta Cryst. 2007, D63, 597-610.
(Reprint)
- McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ:
Phaser crystallographic software
J. Appl. Cryst. 2007, 40, 658-674.
(Reprint)
- Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, Urzhumtsev, A:
On macromolecular refinement at subatomic resolution with
interatomic scatterers
Acta Cryst. 2007, D63, 1194-1197.
(Reprint)
- Bourhis LJ, Grosse-Kunstleve RW, Adams PD:
cctbx news
Newsletter of the IUCr Commission on Crystallographic Computing 2007, 8, 74-80.
(Reprint)
- Adams PD, Afonine, PV, Grosse-Kunstleve RW, Moriarty NW, Sauter NK,
Zwart PH, Gopal K, Ioerger TR, Kanbi L, McKee E, Pai RK, Hung L-W,
Radhakannan T, McCoy AJ, Read RJ, Storoni LC, Romo TD, Sacchettini JC,
Terwilliger TC:
Automated structure determination with Phenix.
In Evolving Methods for Macromolecular Crystallography. Read RJ
and Sussman JL, Eds., Springer, Dordrecht, The Netherlands. 2007,
101-109.
2006
- Sauter NK, Grosse-Kunstleve RW, Adams PD:
Improved statistics for determining the Patterson symmetry from
unmerged diffraction intensities.
J. Appl. Cryst. 2006, 39, 158-168.
(Reprint)
- Zwart PH, Grosse-Kunstleve RW, Adams PD:
Exploring Metric Symmetry
CCP4 newsletter No. 44, Summer 2006.
- Grosse-Kunstleve RW, Zwart PH, Afonine PV, Ioerger TR, Adams PD:
cctbx news
Newsletter of the IUCr Commission on Crystallographic Computing 2006, 7, 92-105.
(Reprint)
2005
- Grosse-Kunstleve RW, Afonine PV, Sauter NK, Adams PD:
cctbx news
Newsletter of the IUCr Commission on Crystallographic Computing 2005, 5, 69-91.
(Reprint)
- McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ:
Likelihood-enhanced fast translation functions
Acta Cryst. 2005, D61, 458-464.
(Reprint)
- Afonine PV, Grosse-Kunstleve RW, Adams PD:
A robust bulk-solvent correction and anisotropic scaling procedure
Acta Cryst. 2005, D61, 850-855.
(Reprint)
- Afonine PV, Grosse-Kunstleve RW, Adams PD:
The Phenix refinement framework
CCP4 newsletter No. 42, Summer 2005.
- Zwart PH, Grosse-Kunstleve RW, Adams PD:
Characterization of X-ray data sets
CCP4 newsletter No. 42, Summer 2005.
- McKee EW, Kanbi LD, Childs KL, Grosse-Kunstleve RW, Adams PD,
Sacchettini JC, Ioerger TR:
FINDMOL: automated identification of macromolecules in
electron-density maps
Acta Cryst. 2005, D61, 1514-1520.
(Reprint)
- Zwart PH, Grosse-Kunstleve RW, Adams PD:
Xtriage and Fest: automatic assessment of X-ray data and
substructure structure factor estimation
CCP4 newsletter No. 43, Winter 2005.
2004
- Grosse-Kunstleve RW, Sauter NK, Adams PD:
Numerically stable algorithms for the computation of
reduced unit cells
Acta Cryst. 2004, A60, 1-6.
(Reprint)
- Grosse-Kunstleve RW, Sauter NK, Adams PD:
cctbx news
Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31.
(Reprint)
- Adams PD, Gopal K, Grosse-Kunstleve RW, Hung L-W, Ioerger TR,
McCoy AJ, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC,
Sauter NK, Storoni LC, Terwilliger TC:
Recent developments in the PHENIX software for automated
crystallographic structure determination.
J. Synchrotron Rad. 2004, 11, 53-55.
(Reprint)
- Sauter NK, Grosse-Kunstleve RW, Adams PD:
Robust indexing for automatic data collection.
J. Appl. Cryst. 2004, 37, 399-409.
(Reprint)
- Grosse-Kunstleve RW, Afonine PV, Adams PD:
cctbx news: Geometry restraints and other new features
Newsletter of the IUCr Commission on Crystallographic Computing 2004, 4, 19-36.
(Reprint)
2003
- Grosse-Kunstleve RW, Adams PD:
State of the Toolbox: an overview of the Computational Crystallography
Toolbox (CCTBX)
Newsletter of the IUCr Commission on Crystallographic Computing 2003, 1, 28-38.
(Reprint)
- Abrahams D, Grosse-Kunstleve RW
Building Hybrid Systems with Boost.Python
C/C++ Users Journal 2003, 21(7):29-36.
- Grosse-Kunstleve RW, Wong B, Adams PD:
cctbx news: Fast triplet generator for direct methods, Gallery of
direct-space asymmetric units, et. al.
Newsletter of the IUCr Commission on Crystallographic Computing 2003, 2, 10-16.
(Reprint)
- Grosse-Kunstleve RW, Adams PD:
Substructure search procedures for macromolecular structures
Acta Cryst. 2003, D59, 1966-1973.
(Reprint)
- Grosse-Kunstleve RW, Adams PD:
On symmetries of substructures
Acta Cryst. 2003, D59, 1974-1977.
(Reprint)
- Weeks CM, Adams PD, Berendzen J, Brunger AT, Dodson EJ,
Grosse-Kunstleve RW, Schneider TR, Sheldrick GM, Terwilliger TC,
Turkenburg MG, Uson I:
Automatic solution of heavy-atom substructures.
Methods Enzymol. 2003, 374, 37-83.
2002
- Grosse-Kunstleve RW, Adams PD:
Algorithms for deriving crystallographic space-group information. II.
Treatment of special positions.
Acta Cryst. 2002, A58, 60-65.
(Reprint)
- Grosse-Kunstleve RW, Sauter NK, Moriarty NW, Adams PD:
The Computational Crystallography Toolbox:
crystallographic algorithms in a reusable software framework.
Journal of Applied Crystallography 2002, 35, 126-136.
(Reprint)
- Grosse-Kunstleve RW, Adams PD:
On the handling of atomic anisotropic displacement parameters.
Journal of Applied Crystallography 2002, 35, 477-480.
(Reprint)
- Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ,
Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger, TC:
PHENIX: building new software for automated crystallographic
structure determination.
Acta Cryst. 2002, D58, 1948-1954.
(Reprint)
2001
- McCusker LB, Baerlocher Ch, Grosse-Kunstleve RW,
Brenner S, Wessels T:
Solving Complex Zeolite Structures from Powder Diffraction Data
Chimia 2001, 55, 497-504.
- Shmueli U, Hall SR, Grosse-Kunstleve RW:
Space-Group Symbols for numeric and symbolic computations.
In International Tables for Crystallography, Volume B: Reciprocal
space, U. Shmueli, Ed., Kluwer
Academic Publishers (Dordrecht), 2001, 107-119.
- Brunger AT, Adams PD, DeLano WL, Gros P, Grosse-Kunstleve RW,
Jiang JS, Pannu NS, Read RJ, Rice LM, Simonson T: The structure
determination language of the Crystallography & NMR System. In
International Tables for Crystallography, Volume F:
Crystallography of biological macromolecules,
M.G. Rossmann and E. Arnold, Eds., Kluwer
Academic Publishers (Dordrecht), 2001, 710-716.
- Grosse-Kunstleve RW, Adams PD:
Patterson correlation methods: a review of
molecular replacement with CNS.
Acta Cryst. 2001, D57, 1390-1396.
(Reprint)
2000
- Adams PD, Grosse-Kunstleve RW:
Recent developments in software
for automation of crystallographic macromolecular structure
determination.
Current Opinion in Structural Biology 2000, 10, 564-568.
- Kirchner RM, Grosse-Kunstleve RW, Pluth JJ, Wilson ST,
Broach RW, Smith JV:
The Structures of As-Synthesized AlPO-53(A), Calcined Dehydrated
AlPO-53(B), and AlPO-53(C), a New Phase Determined by the
FOCUS Method.
Microporous and Mesoporous Materials 2000, 39, 319-332.
1999
1998
- Brunger AT, Adams PD, Clore GM, Gros P, Grosse-Kunstleve RW, Jiang
J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T,
Warren GL:
Crystallography & NMR system (CNS): A new software
system for macromolecular structure determination.
Acta Cryst. 1998, D54, 905-921.
(Reprint)
1997
- Meden A, Grosse-Kunstleve RW, Baerlocher Ch, McCusker LB:
Rietveld Refinement of the as Synthesized and Partially Calcined Forms
of the Molecular Sieve GAPO4-ZON.
Zeitschrift für Kristallographie 1997, 212, 801-807.
- Grosse-Kunstleve RW, McCusker LB, Baerlocher Ch:
Powder Diffraction Data and Crystal Chemical Information Combined in an
Automated Structure Determination Procedure for Zeolites.
Journal of Applied Crystallography 1997, 30, 985-995.
(Reprint)
1996
- Park SH, Grosse-Kunstleve RW, Graetsch H, Gies H:
The thermal expansion of the zeolites MFI, AFI, DOH, DDR, and MTN in
their calcined and as synthesized form.
In Proceedings of the 11th IZA conference 1996, Progress in
Zeolite and Microporous Materials, Studies in Surface Science 105, H.
Chon, S.-K. Ihm, Y.S. Uh, Eds., Elsevier, Amsterdam, 1989-1994 (1996)
- Grosse-Kunstleve RW, Brunner GO, Sloane NJA:
Algebraic Description of Coordination Sequences and Exact
Topological Densities for Zeolites.
Acta Cryst. 1996, A52, 879-889.
(Reprint)
- McCusker LB, Grosse-Kunstleve RW, Baerlocher Ch, Yoshikawa M, Davis ME:
Synthesis Optimization and Structure Analysis of the Zincosilicate
Molecular Sieve VPI-9.
Microporous Materials 1996, 6(5-6):295-309.