Difference between revisions of "Phaser: Manual"

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<div style="margin-left: 25px; float: right;">__TOC__</div>
  
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===Phaser Executable===
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The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].
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Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important.
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*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]
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*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]
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*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]
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*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]
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*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]
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str          string
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int          integer
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float        double precision floating point
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dvect3      array of 3 doubles
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===Python Interface===
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Phaser can be compiled as a python library. The python interface takes a phaser keyword string as input.
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==Basic Keywords==
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===[[Image:User1.gif|link=]]ATOM===
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==Output Control Keywords==
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===[[Image:Output.png|link=]]DEBUG===
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; DEBUG [ON|OFF]
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: Extra verbose output for debugging
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* Default: DEBUG OFF
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==Advanced Keywords==
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===[[Image:User2.gif|link=]]ELLG===
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; ELLG TARGET <TARGET>
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: Target value for expected LLG for determining resolution limits and search order
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<!--; ELLG HIRES <HIRES> Internal control only-->
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* Default: ELLG TARGET 225
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==Expert Keywords==
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===[[Image:Expert.gif|link=]]MACANO===   
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; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
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: Protocol for the refinement of SigmaN in the anisotropy correction
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; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''
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: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.
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* Default: MACANO PROTOCOL DEFAULT
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==Developer Keywords==
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===[[Image:Developer.gif|link=]]BINS===
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; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]
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: The binning of the data.
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: <sup>1</sup> L = minimum number of bins
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: <sup>2</sup> H = maximum number of bins.
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: <sup>3</sup> W = width of the bins in number of reflections

Revision as of 10:39, 9 March 2018

Phaser Executable

The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the MODE keyword. The different modes and the keywords relevant to each mode are described in Modes.

Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important.

str          string
int          integer
float        double precision floating point
dvect3       array of 3 doubles


Python Interface

Phaser can be compiled as a python library. The python interface takes a phaser keyword string as input.



Basic Keywords

User1.gifATOM

Output Control Keywords

Output.pngDEBUG

DEBUG [ON|OFF]
Extra verbose output for debugging
  • Default: DEBUG OFF

Advanced Keywords

User2.gifELLG

ELLG TARGET <TARGET>
Target value for expected LLG for determining resolution limits and search order
  • Default: ELLG TARGET 225



Expert Keywords

Expert.gifMACANO

MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
Protocol for the refinement of SigmaN in the anisotropy correction
MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}
Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.
  • Default: MACANO PROTOCOL DEFAULT


Developer Keywords

Developer.gifBINS

BINS DATA [ 1MIN <L> | 2MAX <H> | 3WIDTH <W> ]
The binning of the data.
1 L = minimum number of bins
2 H = maximum number of bins.
3 W = width of the bins in number of reflections