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Phenix: Difference between revisions
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phenix.ksdssp
(→advanced usage: new nomenclature: optimize_xyz_weight=true optimize_adp_weight=true) |
(phenix.ksdssp) |
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phenix.get_cc_mtz_pdb map_coeffs1.mtz model_2.pdb | phenix.get_cc_mtz_pdb map_coeffs1.mtz model_2.pdb | ||
will create offset.pdb which is a copy of model_2.pdb, adjusted for the origin of map_coeffs_1.mtz, and therefore superimposing on model_1.pdb with space-group symmetry plus allowed origin shifts. This will not change the hand, however. | will create offset.pdb which is a copy of model_2.pdb, adjusted for the origin of map_coeffs_1.mtz, and therefore superimposing on model_1.pdb with space-group symmetry plus allowed origin shifts. This will not change the hand, however. | ||
=== secondary structure analysis === | |||
phenix.ksdssp model.pdb | |||
will output HELIX and SHEET records which you can paste into the PDB header. You should verify the assignments yourself, however, as it occasionally runs adjacent helices together. | |||
== Validation == | == Validation == | ||