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Phenix: Difference between revisions
add phenix.pdb_interpretation
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=== [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics === | === [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics === | ||
e.g. | e.g. | ||
phenix. | phenix.pdbtools your_model.pdb --show-adp-statistics | ||
will show you complete statistics about B-factors; | will show you complete statistics about B-factors; | ||
phenix.pbdtools your_model.pdb --show-geometry-statistics | phenix.pbdtools your_model.pdb --show-geometry-statistics | ||
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phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" | phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" | ||
will set all B=25 for all CA atoms in all ALA residues of chain A. | will set all B=25 for all CA atoms in all ALA residues of chain A. | ||
=== phenix.pdb_interpretation - PDB bonds, distances, dihedrals, ... === | |||
phenix.pdb_interpretation model_1.pdb ligand.cif | |||
will result in a output file model_1.pdb.geo which contains ALL geometry information (bonds, angles, torsions, planarity, non-bonded ...) for each and every atom in your 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/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model === | ||