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PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a | PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a 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 ([http://www.phenix-online.org/ Phenix home page]; [http://www.phenix-online.org/documentation documentation]) has a GUI program (phenix) which can be used to run the programs, but they also work from the command line. | |||
A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return). | |||
* [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 | ||
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* [http://www.phenix-online.org/documentation/xmanip.htm phenix.xmanip] - Structure factor file manipulations | * [http://www.phenix-online.org/documentation/xmanip.htm phenix.xmanip] - Structure factor file manipulations | ||
* [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models | * [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models | ||
* phenix.model_vs_data - not yet documented. | * phenix.model_vs_data - not yet documented. Just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats | ||
* [http://www.phenix-online.org/documentation/fmodel.htm phenix.fmodel] - calculate structure factors from model | * [http://www.phenix-online.org/documentation/fmodel.htm phenix.fmodel] - calculate structure factors from model | ||
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You can find more information about secondary structure restraints in the [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf PHENIX Newsletter] (pages 12-17). | You can find more information about secondary structure restraints in the [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf PHENIX Newsletter] (pages 12-17). | ||
=== [http://www.phenix-online.org/documentation/refinement.htm#anch26 Low resolution refinement] === | |||
Use an existing high resolution model (e.g. in a different spacegroup) for restraining the dihedrals: | |||
phenix.refine data.hkl model.pdb main.reference_model_restraints=True reference_model.file=reference.pdb | |||
The behaviour can be modified with the keywords <font face="Courier">reference_model.limit</font> (default 15 degrees) and <font face="Courier">reference_model.sigma</font> (default probably 1 degrees - the current documentation says 1 Angstrom which is probably not right). | |||
== reciprocal space == | == reciprocal space == | ||
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rigid_body = chain 'L' or chain 'M' | rigid_body = chain 'L' or chain 'M' | ||
} | } | ||
=== [http://www.phenix-online.org/documentation/refinement.htm#anch28 Fix His/Asn/Gln sidechain orientations] === | |||
Use | |||
phenix.refine data.hkl model.pdb main.nqh_flips=True | |||
to automatically flip these sidechains to make them better fit the density and/or hydrogen bonding pattern. | |||
== Atom selection == | == Atom selection == | ||