Hi,
We have experienced the same problem, and what seems to work very well is the following procedure:
1) Add hydrogens to your rebuilt model with phenix.reduce:
phenix.reduce input.pdb > input_h.pdb
2) Minimise the geometry of the protonated model from 1) withOUT X-ray term with:
phenix.geometry_minimization --max-iterations=N input_h.pdb
using a relatively low number of iterations N. You must determine this empirically by trying out a few possibilities, and chosing the highest number of iterations that improves your Molprobity clash score without over-minimising the model, as evidenced by loss of secondary structure. N=100 is a good guess.
3) Feed the geometry-minimised model to phenix.refine, as usual:
phenix.refine input_h_geometry_minimized.pdb ...
As Peter pointed out, this is generally an issue that one encounters at early stages of refinement, when models are still poor; therefore, in most cases you will need to mimimise geometry just once, or during the first cycles of rebuilding only.
HTH,
Luca
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Luca Jovine, Ph.D.
Karolinska Institutet
Department of Biosciences and Nutrition
Hälsovägen 7, S-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290
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On 11 Feb 2008, at 16:01, Simon Kolstoe wrote:
Are there not restraints to prevent steric clashes? In cns I seem to
recall that the energy terms went through the roof if atoms got too
close together.
Secondly, if I remove the clashes through model building and then run
phenix.refine both my R and Rfree go up, and phenix actually puts some
of the clashes back again - does the community accept deposited pdb's
with such obviously poor chemistry?
Simon
On 11 Feb 2008, at 14:51, Peter Zwart wrote:
I am slightly concerned that a refinement program seems happy to
allow
such clashes. Is this a problem with the version of phenix.refine I
am
running, or is there a more obvious explanation that I have missed?
Clash scores are not really used directly in refinement, so the
refinement program doesn't really care about this. Adding hydrogens
could improve the situation a bit, as would some model building do.
How does your starting model look?
HTH
Peter