PMID- 19461840
OWN - NLM
STAT- Publisher
DA  - 20090522
LR  - 20170220
IS  - 0021-8898 (Print)
IS  - 0021-8898 (Linking)
VI  - 40
IP  - Pt 4
DP  - 2007 Aug 01
TI  - Phaser crystallographic software.
PG  - 658-674
AB  - Phaser is a program for phasing macromolecular crystal structures by both
      molecular replacement and experimental phasing methods. The novel phasing
      algorithms implemented in Phaser have been developed using maximum likelihood and
      multivariate statistics. For molecular replacement, the new algorithms have
      proved to be significantly better than traditional methods in discriminating
      correct solutions from noise, and for single-wavelength anomalous dispersion
      experimental phasing, the new algorithms, which account for correlations between 
      F(+) and F(-), give better phases (lower mean phase error with respect to the
      phases given by the refined structure) than those that use mean F and anomalous
      differences DeltaF. One of the design concepts of Phaser was that it be capable
      of a high degree of automation. To this end, Phaser (written in C++) can be
      called directly from Python, although it can also be called using traditional
      CCP4 keyword-style input. Phaser is a platform for future development of improved
      phasing methods and their release, including source code, to the crystallographic
      community.
FAU - McCoy, Airlie J
AU  - McCoy AJ
FAU - Grosse-Kunstleve, Ralf W
AU  - Grosse-Kunstleve RW
FAU - Adams, Paul D
AU  - Adams PD
FAU - Winn, Martyn D
AU  - Winn MD
FAU - Storoni, Laurent C
AU  - Storoni LC
FAU - Read, Randy J
AU  - Read RJ
LA  - eng
GR  - B19543/Biotechnology and Biological Sciences Research Council/United Kingdom
GR  - P01 GM063210/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20070713
PL  - United States
TA  - J Appl Crystallogr
JT  - Journal of applied crystallography
JID - 9876190
PMC - PMC2483472
EDAT- 2007/08/01 00:00
MHDA- 2007/08/01 00:00
CRDT- 2009/05/23 09:00
PHST- 2007/01/31 [received]
PHST- 2007/04/27 [accepted]
AID - 10.1107/S0021889807021206 [doi]
PST - ppublish
SO  - J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674. Epub 2007 Jul 13.

PMID- 16239723
OWN - NLM
STAT- MEDLINE
DA  - 20051021
DCOM- 20051215
LR  - 20091119
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 61
IP  - Pt 11
DP  - 2005 Nov
TI  - A modified ACORN to solve protein structures at resolutions of 1.7 A or better.
PG  - 1465-75
AB  - ACORN has previously been shown to provide an efficient density-modification
      procedure for the solution of protein structures using diffraction data to better
      than 1.3 A. The initial phase set could be obtained from a variety of sources
      such as the position of a heavy atom, a set of scatterers such as S that had been
      positioned from anomalous dispersion measurements, a fragment or a very low
      homology model placed from a molecular-replacement search. Several structures
      solved using the early version of ACORN have been reported in the literature.
      Here, the effect of applying the original ACORN procedures at lower resolution is
      reported and new procedures that yield good-quality maps with data sets of
      resolution down to 1.7 A are described. These new procedures involve the
      artificial extension of data to atomic resolution and new density-modification
      processes that develop density at atomic positions that was previously
      suppressed. The test calculations were aimed firstly towards a proof of principle
      using a small fragment of a known structure to demonstrate that the procedure
      could generate correct density and a derived model in initially empty regions of 
      the cell. Further tests addressed the use of more realistic starting models.
FAU - Jia-xing, Yao
AU  - Jia-xing Y
AD  - York Structural Biology Laboratory, Department of Chemistry, University of York, 
      Heslington, York YO10 5YW, England. yao@ysbl.york.ac.uk
FAU - Woolfson, M M
AU  - Woolfson MM
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 - 20051019
PL  - United States
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Bacterial Proteins)
RN  - 0 (Proteins)
RN  - 0 (pseudoazurin)
RN  - 12284-43-4 (Azurin)
RN  - EC 3.2.1.- (Mannosidases)
RN  - EC 3.4.23.- (Aspartic Acid Endopeptidases)
RN  - EC 3.6.1.- (Pyrophosphatases)
RN  - EC 3.6.1.23 (dUTP pyrophosphatase)
SB  - IM
MH  - *Algorithms
MH  - Aspartic Acid Endopeptidases/chemistry
MH  - Azurin/chemistry
MH  - Bacterial Proteins/chemistry
MH  - Crystallography, X-Ray/*methods
MH  - Data Interpretation, Statistical
MH  - Mannosidases/chemistry
MH  - Models, Molecular
MH  - Proteins/*chemistry
MH  - Pyrophosphatases/chemistry
EDAT- 2005/10/22 09:00
MHDA- 2005/12/16 09:00
CRDT- 2005/10/22 09:00
PHST- 2005/06/14 [received]
PHST- 2005/08/11 [accepted]
AID - S090744490502576X [pii]
AID - 10.1107/S090744490502576X [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2005 Nov;61(Pt 11):1465-75. Epub 2005 Oct
      19.