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Phenix: Difference between revisions
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PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a new software suite for the automated determination and refinement of macromolecular structures using X-ray crystallography and other methods. It integrates well with CCP4-formatted files for I/O, is highly automated, and very straightforward to use. | PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a new software suite for the automated determination and refinement of macromolecular structures using X-ray crystallography and other methods. It integrates well with CCP4-formatted files for I/O, is highly automated, and very straightforward to use. | ||
The suite has a GUI program (phenix) which can be used to run the programs: | The suite has a GUI program (phenix) which can be used to run the programs, but they also work from the command line: | ||
* [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] - refinement program | * [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] - refinement program | ||
* [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality | * [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality | ||
* [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map | * [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map | ||
* ... | * [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics; e.g. <font face="Courier">phenix.pbdtools your_model.pdb --show-adp-statistics</font> will show you complete statistics about B-factors; <font face="Courier">phenix.pbdtools your_model.pdb --show-geometry-statistics</font> will show you complete statistics about stereochemistry, and so on | ||
* ... | * ... | ||