[phenixbb] Clashes problem

Luca Jovine luca.jovine at biosci.ki.se
Mon Feb 11 07:26:49 PST 2008


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.



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
E-mail: luca.jovine at ki.se
W3: http://www.biosci.ki.se/groups/ljo/

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
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