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Phaser crystallographic software.

McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ - J Appl Crystallogr (2007)

Bottom Line: The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics.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.

View Article: PubMed Central - HTML - PubMed

ABSTRACT
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.

No MeSH data available.


Flow diagram for automated molecular replacement in Phaser.
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fig1: Flow diagram for automated molecular replacement in Phaser.

Mentions: Most structures that can be solved by MR with Phaser can be solved using the ‘automated molecular replacement’ mode. The flow diagram for this mode is shown in Fig. 1 ▶. The search strategy automates four search processes: those for multiple components in the asymmetric unit, for ambiguity in the hand of the space group and/or other space groups in the same point group, for permutations in the search order for components (when there are multiple components), and for finding the best model when there is more than one possible model for a component.


Phaser crystallographic software.

McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ - J Appl Crystallogr (2007)

Flow diagram for automated molecular replacement in Phaser.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483472&req=5

fig1: Flow diagram for automated molecular replacement in Phaser.
Mentions: Most structures that can be solved by MR with Phaser can be solved using the ‘automated molecular replacement’ mode. The flow diagram for this mode is shown in Fig. 1 ▶. The search strategy automates four search processes: those for multiple components in the asymmetric unit, for ambiguity in the hand of the space group and/or other space groups in the same point group, for permutations in the search order for components (when there are multiple components), and for finding the best model when there is more than one possible model for a component.

Bottom Line: The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics.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.

View Article: PubMed Central - HTML - PubMed

ABSTRACT
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.

No MeSH data available.