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Phenix: Difference between revisions
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add phenix.reduce, occupancy, mailing list
m (add phenix.elbow link) |
m (add phenix.reduce, occupancy, mailing list) |
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* [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 | * [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 | ||
* [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 | |||
* ... | * ... | ||
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will produce all_ligands.cif, which may be fed to phenix.refine by | will produce all_ligands.cif, which may be fed to phenix.refine by | ||
phenix.refine model.pdb data.mtz all_ligands.cif ... | phenix.refine model.pdb data.mtz all_ligands.cif ... | ||
== Occupancy refinement | |||
Adding "occupancy" to the "strategy" options will refine the occupancies of those parts of the model that have alternate conformations. | |||
== NCS == | == NCS == | ||
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[http://www.phenix-online.org/ Phenix home page] | [http://www.phenix-online.org/ Phenix home page] | ||
[http://www.phenix-online.org/pipermail/phenixbb/ Phenix mailing list] | |||