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Phenix: Difference between revisions
remove duplicate pdbtools example, add phenix.explore_metric_symmetry
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* [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 | * [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, <font face="Courier">phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" </font>- this will set all B=25 for all CA atoms in all ALA residues of chain A. | ||
* [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench | * [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench | ||
* [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model | * [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model | ||
* [http://www.phenix-online.org/documentation/ | * [http://www.phenix-online.org/documentation/explore_metric_symmetry.htm phenix.explore_metric_symmetry] <font face="Courier">--unit_cell=145,44,67,90,110.5,90 --space_group=C2 --other_unit_cell=67,44,136,90,96,90 --other_space_group=p2</font> - investigate different settings | ||
== Example == | == Example for use of phenix.refine == | ||
phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ | phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ | ||