PMID- 22505253
OWN - NLM
STAT- MEDLINE
DA  - 20120416
DCOM- 20120619
LR  - 20141016
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 68
IP  - Pt 4
DP  - 2012 Apr
TI  - Completion of autobuilt protein models using a database of protein fragments.
PG  - 328-35
LID - 10.1107/S0907444911039655 [doi]
AB  - Two developments in the process of automated protein model building in the
      Buccaneer software are presented. A general-purpose library for protein fragments
      of arbitrary size is described, with a highly optimized search method allowing
      the use of a larger database than in previous work. The problem of assembling an 
      autobuilt model into complete chains is discussed. This involves the assembly of 
      disconnected chain fragments into complete molecules and the use of the database 
      of protein fragments in improving the model completeness. Assembly of fragments
      into molecules is a standard step in existing model-building software, but the
      methods have not received detailed discussion in the literature.
FAU - Cowtan, Kevin
AU  - Cowtan K
AD  - Department of Chemistry, University of York, Heslington, York YO10 5DD, England. 
      cowtan@ysbl.york.ac.uk
LA  - eng
GR  - BB/F0202281/Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20120316
PL  - United States
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Peptide Fragments)
SB  - IM
MH  - Crystallography, X-Ray
MH  - *Databases, Protein
MH  - Models, Molecular
MH  - Peptide Fragments/*chemistry
MH  - Protein Structure, Tertiary
MH  - Software
PMC - PMC3322592
OID - NLM: PMC3322592
EDAT- 2012/04/17 06:00
MHDA- 2012/06/20 06:00
CRDT- 2012/04/17 06:00
PHST- 2011/06/02 [received]
PHST- 2011/09/27 [accepted]
PHST- 2012/03/16 [epublish]
AID - S0907444911039655 [pii]
AID - 10.1107/S0907444911039655 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):328-35. doi:10.1107/S0907444911039655. Epub 2012 Mar 16.

PMID- 16929101
OWN - NLM
STAT- MEDLINE
DA  - 20060824
DCOM- 20070116
LR  - 20070724
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 62
IP  - Pt 9
DP  - 2006 Sep
TI  - The Buccaneer software for automated model building. 1. Tracing protein chains.
PG  - 1002-11
AB  - A new technique for the automated tracing of protein chains in experimental
      electron-density maps is described. The technique relies on the repeated
      application of an oriented electron-density likelihood target function to
      identify likely C(alpha) positions. This function is applied both in the location
      of a few promising ;seed' positions in the map and to grow those initial C(alpha)
      positions into extended chain fragments. Techniques for assembling the chain
      fragments into an initial chain trace are discussed.
FAU - Cowtan, Kevin
AU  - Cowtan K
AD  - Department of Chemistry, University of York, Heslington, York YO10 5DD, England. 
      cowtan@ysbl.york.ac.uk
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20060819
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
RN  - EC 1.- (Mixed Function Oxygenases)
RN  - EC 1.14.11.- (aspartic acid 2-oxoglutarate-dependent dioxygenase)
SB  - IM
MH  - Algorithms
MH  - Automation
MH  - Bacillus subtilis/enzymology
MH  - Computational Biology/*methods
MH  - Crystallography, X-Ray
MH  - Mixed Function Oxygenases/chemistry
MH  - Models, Molecular
MH  - Models, Statistical
MH  - Models, Theoretical
MH  - Molecular Conformation
MH  - Probability
MH  - Proteins/*chemistry
MH  - Proteomics/methods
MH  - *Software
EDAT- 2006/08/25 09:00
MHDA- 2007/01/17 09:00
CRDT- 2006/08/25 09:00
PHST- 2006/08/19 [epublish]
AID - S0907444906022116 [pii]
AID - 10.1107/S0907444906022116 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11. Epub 2006 Aug 19.

PMID- 29533229
AU  - O.  Kovalevskiy, R. A.  Nicholls, F.  Long, A.  Carlon and G. N.  Murshudov
TI  - Overview of refinement procedures within REFMAC5: utilizing data from different sources
SO  - Acta Crystallographica Section D 2018;74(3):
UR  - https://doi.org/10.1107/S2059798318000979
N1  - doi:10.1107/S2059798318000979

PMID- 21460454
OWN - NLM
STAT- MEDLINE
DA  - 20110404
DCOM- 20110627
LR  - 20131018
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 67
IP  - Pt 4
DP  - 2011 Apr
TI  - REFMAC5 for the refinement of macromolecular crystal structures.
PG  - 355-67
LID - 10.1107/S0907444911001314 [doi]
AB  - This paper describes various components of the macromolecular crystallographic
      refinement program REFMAC5, which is distributed as part of the CCP4 suite.
      REFMAC5 utilizes different likelihood functions depending on the diffraction data
      employed (amplitudes or intensities), the presence of twinning and the
      availability of SAD/SIRAS experimental diffraction data. To ensure chemical and
      structural integrity of the refined model, REFMAC5 offers several classes of
      restraints and choices of model parameterization. Reliable models at resolutions 
      at least as low as 4 A can be achieved thanks to low-resolution refinement tools 
      such as secondary-structure restraints, restraints to known homologous
      structures, automatic global and local NCS restraints, `jelly-body' restraints
      and the use of novel long-range restraints on atomic displacement parameters
      (ADPs) based on the Kullback-Leibler divergence. REFMAC5 additionally offers TLS 
      parameterization and, when high-resolution data are available, fast refinement of
      anisotropic ADPs. Refinement in the presence of twinning is performed in a fully 
      automated fashion. REFMAC5 is a flexible and highly optimized refinement package 
      that is ideally suited for refinement across the entire resolution spectrum
      encountered in macromolecular crystallography.
FAU - Murshudov, Garib N
AU  - Murshudov GN
AD  - Structural Biology Laboratory, Department of Chemistry, University of York,
      Heslington, York, England. garib@ysbl.york.ac.uk
FAU - Skubak, Pavol
AU  - Skubak P
FAU - Lebedev, Andrey A
AU  - Lebedev AA
FAU - Pannu, Navraj S
AU  - Pannu NS
FAU - Steiner, Roberto A
AU  - Steiner RA
FAU - Nicholls, Robert A
AU  - Nicholls RA
FAU - Winn, Martyn D
AU  - Winn MD
FAU - Long, Fei
AU  - Long F
FAU - Vagin, Alexei A
AU  - Vagin AA
LA  - eng
GR  - 064405/Z/01/A/Wellcome Trust/United Kingdom
GR  - BB/F0202281/Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110318
PL  - England
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
SB  - IM
MH  - Anisotropy
MH  - Crystallography, X-Ray/*methods
MH  - Likelihood Functions
MH  - *Software
PMC - PMC3069751
OID - NLM: PMC3069751
EDAT- 2011/04/05 06:00
MHDA- 2011/06/28 06:00
CRDT- 2011/04/05 06:00
PHST- 2010/07/14 [received]
PHST- 2011/01/10 [accepted]
PHST- 2011/03/18 [epublish]
AID - S0907444911001314 [pii]
AID - 10.1107/S0907444911001314 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. doi:10.1107/S0907444911001314. Epub 2011 Mar 18.
URL - http://www.ncbi.nlm.nih.gov/pubmed/21460454

PMID- 15299926
OWN - NLM
STAT- PubMed-not-MEDLINE
DA  - 20040809
DCOM- 20050217
LR  - 20070724
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 53
IP  - Pt 3
DP  - 1997 May 1
TI  - Refinement of macromolecular structures by the maximum-likelihood method.
PG  - 240-55
AB  - This paper reviews the mathematical basis of maximum likelihood. The likelihood
      function for macromolecular structures is extended to include prior phase
      information and experimental standard uncertainties. The assumption that
      different parts of a structure might have different errors is considered. A
      method for estimating sigma(A) using 'free' reflections is described and its
      effects analysed. The derived equations have been implemented in the program
      REFMAC. This has been tested on several proteins at different stages of
      refinement (bacterial alpha-amylase, cytochrome c', cross-linked insulin and
      oligopeptide binding protein). The results derived using the maximum-likelihood
      residual are consistently better than those obtained from least-squares
      refinement.
FAU - Murshudov, G N
AU  - Murshudov GN
AD  - Chemistry Department, University of York, Heslington, England.
FAU - Vagin, A A
AU  - Vagin AA
FAU - Dodson, E J
AU  - Dodson EJ
LA  - eng
PT  - Journal Article
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
EDAT- 1997/05/01 00:00
MHDA- 1997/05/01 00:01
CRDT- 1997/05/01 00:00
AID - 10.1107/S0907444996012255 [doi]
AID - S0907444996012255 [pii]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55.

PMID- 22505260
OWN - NLM
STAT- MEDLINE
DA  - 20120416
DCOM- 20120619
LR  - 20140220
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 68
IP  - Pt 4
DP  - 2012 Apr
TI  - Low-resolution refinement tools in REFMAC5.
PG  - 404-17
LID - 10.1107/S090744491105606X [doi]
AB  - Two aspects of low-resolution macromolecular crystal structure analysis are
      considered: (i) the use of reference structures and structural units for
      provision of structural prior information and (ii) map sharpening in the presence
      of noise and the effects of Fourier series termination. The generation of
      interatomic distance restraints by ProSMART and their subsequent application in
      REFMAC5 is described. It is shown that the use of such external structural
      information can enhance the reliability of derived atomic models and stabilize
      refinement. The problem of map sharpening is considered as an inverse deblurring 
      problem and is solved using Tikhonov regularizers. It is demonstrated that this
      type of map sharpening can automatically produce a map with more structural
      features whilst maintaining connectivity. Tests show that both of these
      directions are promising, although more work needs to be performed in order to
      further exploit structural information and to address the problem of reliable
      electron-density calculation.
FAU - Nicholls, Robert A
AU  - Nicholls RA
AD  - Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2
      0QH, England.
FAU - Long, Fei
AU  - Long F
FAU - Murshudov, Garib N
AU  - Murshudov GN
LA  - eng
GR  - MC_UP_A025_1012/Medical Research Council/United Kingdom
GR  - MC_US_A025_0104/Medical Research Council/United Kingdom
GR  - Biotechnology and Biological Sciences Research Council/United Kingdom
GR  - Wellcome Trust/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20120316
PL  - United States
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
SB  - IM
MH  - Crystallography, X-Ray/*methods
MH  - Models, Molecular
MH  - Protein Structure, Secondary
MH  - Protein Structure, Tertiary
MH  - Proteins/analysis/chemistry
PMC - PMC3322599
OID - NLM: PMC3322599
EDAT- 2012/04/17 06:00
MHDA- 2012/06/20 06:00
CRDT- 2012/04/17 06:00
PHST- 2011/11/02 [received]
PHST- 2011/12/28 [accepted]
PHST- 2012/03/16 [epublish]
AID - S090744491105606X [pii]
AID - 10.1107/S090744491105606X [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):404-17. doi:10.1107/S090744491105606X. Epub 2012 Mar 16.

PMID- 15572771
OWN - NLM
STAT- MEDLINE
DA  - 20041201
DCOM- 20050222
LR  - 20081121
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 60
IP  - Pt 12 Pt 1
DP  - 2004 Dec
TI  - REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for
      its use.
PG  - 2184-95
AB  - One of the most important aspects of macromolecular structure refinement is the
      use of prior chemical knowledge. Bond lengths, bond angles and other chemical
      properties are used in restrained refinement as subsidiary conditions. This
      contribution describes the organization and some aspects of the use of the
      flexible and human/machine-readable dictionary of prior chemical knowledge used
      by the maximum-likelihood macromolecular-refinement program REFMAC5. The
      dictionary stores information about monomers which represent the constitutive
      building blocks of biological macromolecules (amino acids, nucleic acids and
      saccharides) and about numerous organic/inorganic compounds commonly found in
      macromolecular crystallography. It also describes the modifications the building 
      blocks undergo as a result of chemical reactions and the links required for
      polymer formation. More than 2000 monomer entries, 100 modification entries and
      200 link entries are currently available. Algorithms and tools for updating and
      adding new entries to the dictionary have also been developed and are presented
      here. In many cases, the REFMAC5 dictionary allows entirely automatic generation 
      of restraints within REFMAC5 refinement runs.
FAU - Vagin, Alexei A
AU  - Vagin AA
AD  - Structural Biology Laboratory, Department of Chemistry, University of York, York 
      YO10 5YW, England.
FAU - Steiner, Roberto A
AU  - Steiner RA
FAU - Lebedev, Andrey A
AU  - Lebedev AA
FAU - Potterton, Liz
AU  - Potterton L
FAU - McNicholas, Stuart
AU  - McNicholas S
FAU - Long, Fei
AU  - Long F
FAU - Murshudov, Garib N
AU  - Murshudov GN
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20041126
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Peptide Library)
RN  - 0 (Proteins)
SB  - IM
MH  - Chemical Phenomena
MH  - Chemistry
MH  - *Computational Biology
MH  - Crystallography, X-Ray
MH  - Dictionaries as Topic
MH  - Internet
MH  - Models, Molecular
MH  - Peptide Library
MH  - Protein Conformation
MH  - Proteins/*chemistry
MH  - *Software
EDAT- 2004/12/02 09:00
MHDA- 2005/02/23 09:00
CRDT- 2004/12/02 09:00
PHST- 2004/04/19 [received]
PHST- 2004/09/22 [accepted]
PHST- 2004/11/26 [epublish]
AID - S0907444904023510 [pii]
AID - 10.1107/S0907444904023510 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2184-95. Epub 2004
      Nov 26.

PMID- 10089417
OWN - NLM
STAT- MEDLINE
DA  - 19990503
DCOM- 19990503
LR  - 20070724
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 55
IP  - Pt 1
DP  - 1999 Jan
TI  - Efficient anisotropic refinement of macromolecular structures using FFT.
PG  - 247-55
AB  - This paper gives the equations for the use of fast Fourier transformations in
      individual atomic anisotropic refinement. Restraints on bonded atoms, on the
      sphericity of each atom and between non-crystallographic symmetry related atoms
      are described. These have been implemented in the program REFMAC and its
      performance with several examples is analysed. All the tests show that
      anisotropic refinement not only reduces the R value and Rfree but also improves
      the fit to geometric targets, indicating that this parameterization is valuable
      for improving models derived from experimental data. The computer time taken is
      comparable to that for isotropic refinements.
FAU - Murshudov, G N
AU  - Murshudov GN
AD  - Chemistry Department, University of York, Heslington, York YO1 5DD, England and
      CLRC, Daresbury Laboratory, Daresbury, Warrington WA4 4AD,
      England.garib@yorvic.york.ac.uk
FAU - Vagin, A A
AU  - Vagin AA
FAU - Lebedev, A
AU  - Lebedev A
FAU - Wilson, K S
AU  - Wilson KS
FAU - Dodson, E J
AU  - Dodson EJ
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 19990101
PL  - DENMARK
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Macromolecular Substances)
RN  - EC 1.11.1.6 (Catalase)
RN  - EC 3.1.- (Ribonucleases)
SB  - IM
MH  - Catalase/chemistry
MH  - *Crystallography, X-Ray
MH  - *Fluorescence Polarization
MH  - *Fourier Analysis
MH  - Macromolecular Substances
MH  - Models, Molecular
MH  - Protein Conformation
MH  - Ribonucleases/chemistry
MH  - Software
EDAT- 1999/03/25 03:01
MHDA- 2000/06/23 11:00
CRDT- 1999/03/25 03:01
PHST- 1998/10/02 [received]
PHST- 1998/10/25 [accepted]
PHST- 1999/01/01 [epublish]
AID - 10.1107/S090744499801405X [doi]
AID - S090744499801405X [pii]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):247-55. Epub 1999 Jan 1.

PMID- 14696379
OWN - NLM
STAT- MEDLINE
DA  - 20031230
DCOM- 20040204
LR  - 20091119
IS  - 0076-6879 (Print)
IS  - 0076-6879 (Linking)
VI  - 374
DP  - 2003
TI  - Macromolecular TLS refinement in REFMAC at moderate resolutions.
PG  - 300-21
FAU - Winn, Martyn D
AU  - Winn MD
AD  - Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, United Kingdom.
FAU - Murshudov, Garib N
AU  - Murshudov GN
FAU - Papiz, Miroslav Z
AU  - Papiz MZ
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Methods Enzymol
JT  - Methods in enzymology
JID - 0212271
RN  - 0 (Proteins)
SB  - IM
MH  - Chemistry Techniques, Analytical/*methods
MH  - Crystallography, X-Ray/methods
MH  - *Data Interpretation, Statistical
MH  - Likelihood Functions
MH  - Models, Molecular
MH  - Protein Structure, Tertiary
MH  - Proteins/*chemistry
MH  - *Software
EDAT- 2003/12/31 05:00
MHDA- 2004/02/05 05:00
CRDT- 2003/12/31 05:00
AID - 10.1016/S0076-6879(03)74014-2 [doi]
AID - S0076687903740142 [pii]
PST - ppublish
SO  - Methods Enzymol. 2003;374:300-21.

PMID- 20057045
OWN - NLM
STAT- MEDLINE
DA  - 20100108
DCOM- 20100624
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 66
IP  - Pt 1
DP  - 2010 Jan
TI  - Molecular replacement with MOLREP.
PG  - 22-5
LID - 10.1107/S0907444909042589 [doi]
AB  - MOLREP is an automated program for molecular replacement that utilizes a number
      of original approaches to rotational and translational search and data
      preparation. Since the first publication describing the program, MOLREP has
      acquired a variety of features that include weighting of the X-ray data and
      search models, multi-copy search, fitting the model into electron density,
      structural superposition of two models and rigid-body refinement. The program can
      run in a fully automatic mode using optimized parameters calculated from the
      input data.
FAU - Vagin, Alexei
AU  - Vagin A
AD  - Structural Biology Laboratory, University of York, Heslington, York YO10 5YW,
      England. alexei@ysbl.york.ac.uk
FAU - Teplyakov, Alexei
AU  - Teplyakov A
LA  - eng
GR  - Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20091221
PL  - England
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
SB  - IM
MH  - Automatic Data Processing
MH  - Crystallization
MH  - Crystallography, X-Ray/*methods
MH  - Models, Chemical
MH  - Molecular Conformation
MH  - Search Engine
MH  - *Software
EDAT- 2010/01/09 06:00
MHDA- 2010/06/25 06:00
CRDT- 2010/01/09 06:00
PHST- 2009/07/09 [received]
PHST- 2009/10/13 [accepted]
PHST- 2009/12/21 [epublish]
AID - S0907444909042589 [pii]
AID - 10.1107/S0907444909042589 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):22-5. doi:10.1107/S0907444909042589. Epub 2009 Dec 21.

PMID- 18094465
OWN - NLM
STAT- MEDLINE
DA  - 20071220
DCOM- 20080331
LR  - 20130903
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 64
IP  - Pt 1
DP  - 2008 Jan
TI  - Model preparation in MOLREP and examples of model improvement using X-ray data.
PG  - 33-9
AB  - The success of molecular replacement is critically dependent on the quality of
      the search model. Several model-preparation procedures are integrated in the
      molecular-replacement program MOLREP. These include model modification on the
      basis of amino-acid sequence alignment and model correction based on analysis of 
      the solvent-accessibility of the atoms. The packing function used in MOLREP for
      the translational search is explained in the context of model preparation. In
      difficult cases, bioinformatics-based modifications are not sufficient for
      successful molecular replacement. An approach implemented in MOLREP for solving
      cases with translational noncrystallographic symmetry is an example of model
      preparation in which analysis of X-ray data plays an essential role. In addition,
      two examples are presented in which the X-ray data were used to refine partial
      models for subsequent use in molecular replacement.
FAU - Lebedev, Andrey A
AU  - Lebedev AA
AD  - Structural Biology Laboratory, Department of Chemistry, University of York,
      Heslington, York YO10 5YW, England. lebedev@ysbl.york.ac.uk
FAU - Vagin, Alexei A
AU  - Vagin AA
FAU - Murshudov, Garib N
AU  - Murshudov GN
LA  - eng
GR  - 064405/Z/01/A/Wellcome Trust/United Kingdom
GR  - R01 GM069758-03/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20071205
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
SB  - IM
MH  - Algorithms
MH  - Amino Acid Sequence
MH  - *Computer Simulation
MH  - Crystallization
MH  - Crystallography, X-Ray/*methods
MH  - Models, Molecular
MH  - Proteins/chemistry/genetics
MH  - Sequence Alignment
MH  - *Software
MH  - Structural Homology, Protein
PMC - PMC2394799
OID - NLM: PMC2394799
EDAT- 2007/12/21 09:00
MHDA- 2008/04/01 09:00
CRDT- 2007/12/21 09:00
PHST- 2007/06/09 [received]
PHST- 2007/10/10 [accepted]
PHST- 2007/12/05 [epublish]
AID - S0907444907049839 [pii]
AID - 10.1107/S0907444907049839 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):33-9. Epub 2007 Dec 5.

PMID- 18094475
AU  - R. M.  Keegan and M. D.  Winn
TI  - MrBUMP: an automated pipeline for molecular replacement
SO  - Acta Crystallographica Section D 2008;64(1):119-124
UR  - http://dx.doi.org/10.1107/S0907444907037195
N1  - doi:10.1107/S0907444907037195

PMID- 23793146
OWN - NLM
STAT- MEDLINE
DA  - 20130624
DCOM- 20131017
LR  - 20140220
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 69
IP  - Pt 7
DP  - 2013 Jul
TI  - How good are my data and what is the resolution?
PG  - 1204-14
LID - 10.1107/S0907444913000061 [doi]
AB  - Following integration of the observed diffraction spots, the process of `data
      reduction' initially aims to determine the point-group symmetry of the data and
      the likely space group. This can be performed with the program POINTLESS. The
      scaling program then puts all the measurements on a common scale, averages
      measurements of symmetry-related reflections (using the symmetry determined
      previously) and produces many statistics that provide the first important
      measures of data quality. A new scaling program, AIMLESS, implements scaling
      models similar to those in SCALA but adds some additional analyses. From the
      analyses, a number of decisions can be made about the quality of the data and
      whether some measurements should be discarded. The effective `resolution' of a
      data set is a difficult and possibly contentious question (particularly with
      referees of papers) and this is discussed in the light of tests comparing the
      data-processing statistics with trials of refinement against observed and
      simulated data, and automated model-building and comparison of maps calculated
      with different resolution limits. These trials show that adding weak
      high-resolution data beyond the commonly used limits may make some improvement
      and does no harm.
FAU - Evans, Philip R
AU  - Evans PR
AD  - MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England.
      pre@mrc-lmb.cam.ac.uk
FAU - Murshudov, Garib N
AU  - Murshudov GN
LA  - eng
GR  - MC_U105178845/Medical Research Council/United Kingdom
GR  - MC_UP_A025_1012/Medical Research Council/United Kingdom
GR  - U105178845/Medical Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20130613
PL  - United States
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
SB  - IM
MH  - *Algorithms
MH  - Anisotropy
MH  - Computer Simulation
MH  - *Crystallography, X-Ray
MH  - *Data Interpretation, Statistical
MH  - *Image Interpretation, Computer-Assisted
MH  - Models, Molecular
MH  - Software
PMC - PMC3689523
OID - NLM: PMC3689523
OTO - NOTNLM
OT  - data reduction
OT  - data scaling
OT  - data statistics
OT  - software
EDAT- 2013/06/26 06:00
MHDA- 2013/10/18 06:00
CRDT- 2013/06/25 06:00
PHST- 2012/09/07 [received]
PHST- 2013/01/02 [accepted]
PHST- 2013/06/13 [epublish]
AID - S0907444913000061 [pii]
AID - 10.1107/S0907444913000061 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2013 Jul;69(Pt 7):1204-14. doi:10.1107/S0907444913000061. Epub 2013 Jun 13.

PMID- 21460446
OWN - NLM
STAT- MEDLINE
DA  - 20110404
DCOM- 20110627
LR  - 20141105
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 67
IP  - Pt 4
DP  - 2011 Apr
TI  - An introduction to data reduction: space-group determination, scaling and
      intensity statistics.
PG  - 282-92
LID - 10.1107/S090744491003982X [doi]
AB  - This paper presents an overview of how to run the CCP4 programs for data
      reduction (SCALA, POINTLESS and CTRUNCATE) through the CCP4 graphical interface
      ccp4i and points out some issues that need to be considered, together with a few 
      examples. It covers determination of the point-group symmetry of the diffraction 
      data (the Laue group), which is required for the subsequent scaling step,
      examination of systematic absences, which in many cases will allow inference of
      the space group, putting multiple data sets on a common indexing system when
      there are alternatives, the scaling step itself, which produces a large set of
      data-quality indicators, estimation of |F| from intensity and finally examination
      of intensity statistics to detect crystal pathologies such as twinning. An
      appendix outlines the scoring schemes used by the program POINTLESS to assign
      probabilities to possible Laue and space groups.
FAU - Evans, Philip R
AU  - Evans PR
AD  - MRC Laboratory of Molecular Biology, Cambridge, England. pre@mrc-lmb.cam.ac.uk
LA  - eng
GR  - BB/F020228/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
GR  - MC_G0900846/Medical Research Council/United Kingdom
GR  - MC_U105178845/Medical Research Council/United Kingdom
PT  - Journal Article
DEP - 20110318
PL  - England
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
SB  - IM
MH  - Crystallography, X-Ray/*methods
MH  - *Numerical Analysis, Computer-Assisted
MH  - Probability
MH  - Software
PMC - PMC3069743
OID - NLM: PMC3069743
EDAT- 2011/04/05 06:00
MHDA- 2011/06/28 06:00
CRDT- 2011/04/05 06:00
PHST- 2010/08/04 [received]
PHST- 2010/10/05 [accepted]
PHST- 2011/03/18 [epublish]
AID - S090744491003982X [pii]
AID - 10.1107/S090744491003982X [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):282-92. doi:10.1107/S090744491003982X. Epub 2011 Mar 18.
