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Phenix: Difference between revisions
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* [http://www.phenix-online.org/documentation/reflection_statistics.htm phenix.reflection_statistics] - compare datasets (in 1 or 2 files) | * [http://www.phenix-online.org/documentation/reflection_statistics.htm phenix.reflection_statistics] - compare datasets (in 1 or 2 files) | ||
* [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] | * [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models | ||
* phenix.model_vs_data - not yet documented. Pavel says: just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats. And if you need a little extra, such as specify your data type (X-ray or neutron), or data labels (in case your data file has multiple data sets), just do what is supported in all PHENIX command line tools: type phenix.model_vs_data and hit Enter (or Return) and you will get a quick message about usage and options. Also, there is a dedicated paper that came out recently: Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics J. Appl. Cryst. 2010, 43, 669-676 | * phenix.model_vs_data - not yet documented. Pavel says: just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats. And if you need a little extra, such as specify your data type (X-ray or neutron), or data labels (in case your data file has multiple data sets), just do what is supported in all PHENIX command line tools: type phenix.model_vs_data and hit Enter (or Return) and you will get a quick message about usage and options. Also, there is a dedicated paper that came out recently: Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics J. Appl. Cryst. 2010, 43, 669-676 | ||
* [http://www.phenix-online.org/documentation/fmodel.htm phenix.fmodel] | * [http://www.phenix-online.org/documentation/fmodel.htm phenix.fmodel] - calculate structure factors from model | ||
Below, the most important hints for the use of [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] are given. | |||
== Example for use of phenix.refine == | == Example for use of phenix.refine == | ||