[phenixbb] Question about restraints
Ralf W. Grosse-Kunstleve
rwgk at yahoo.com
Fri Nov 12 16:18:02 PST 2010
Hi Carsten,
> yes ligand has good geometry initially, i.e. after I generate it. During
> placement in coot and refinement in phenix it gets a bit distorted. In
> general I see these kind of problems in saturated, substituted ring
> systems using medium resolution < 2.0 A. The density is not clear enough
> to restrict the conformations of these ring systems, since it is
> basically enclosed in a round blob of density. So the real space
> refinement in coot and refinement in phenix take liberty from the
> freedom given in the restraints (Sorry had to paraphrase DVD here...) to
> fit the ligand in the ambiguous density.
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.
Ralf
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