[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 


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