Phenix: Difference between revisions

Phenix (edit)

1,333 bytes added , 14 November 2010

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+== Refinement with mmtbx.lockit ==
+From RWGK's posting to [http://www.phenix-online.org/mailman/listinfo/phenixbb phenixbb] on Nov 14, 2010:
+We have a tool for quick real-space refinement that's geared towards making the
+geometry ideal in the end. I'm not sure it is useful in your situation, but may
+be worth a try. It works like this:
+ mmtbx.lockit your.pdb your_refine_001_map_coeffs.mtz \
+       map.coeff_labels.f=2FOFCWT,PH2FOFCWT coordinate_refinement.run=True \
+       atom_selection='resname LIG'
+It works in two stages. First it attempts to maximize the real-space weight
+allowing for a significant (but not totally unreasonable) distortion of the
+geometry. This is meant to move the ligand into the density. In the second stage
+it scales down the "best" real-space weight and runs a number of real-space
+refinements until the selected atoms do not move anymore. The expected result is
+nearly ideal geometry.
+The procedure is usually very quick. If it turns out to be useful we could
+integrate it into phenix.refine, to be run after reciprocal-space refinement.
+The mmtbx.lockit command is not as user-friendly as phenix.refine. It only works
+with mtz files, you have to manually specify the mtz labels, and the error
+messages may be unhelpful. Also be sure there is a valid CRYST1 card in your pdb
+file.
 == Maps ==