Phenix: Difference between revisions

303 bytes added ,  3 December 2010
add phenix.pdb_interpretation
(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.pbdtools your_model.pdb --show-adp-statistics
  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 ===
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