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

...

Thanks,

Simon _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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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 ------------------------------------------------ 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: [email protected] 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

Hi Jianghai, the answers to both of your questions are YES: - running phenix.refine with "wxc_scale=0" is essentially the same as performing a pure geometry regularization (no Xray contribution is accounted for). It is just less time efficient since even if you say "wxc_scale=0", phenix.refine still compute all X-ray related things like X-ray targets, R-factors, do bulk-solvent correction etc... - yes, phenix.refine will use all your custom bond definitions regardless the value of "wxc_scale" parameter. Pavel. On 2/11/2008 12:43 PM, Jianghai Zhu wrote:

...

2) Minimise the geometry of the protonated model from 1) withOUT X- ray term with:

phenix.geometry_minimization --max-iterations=N input_h.pdb

I have a question about geometry_minimization. I think wxc_scale = 0 is the same as phenix.geometry_minimization. But I have some external bond definitions defined in the eff file. So if I use wxc_scale = 0 and phenix.refine, will those external bonds be imposed on the model as the default geometries?

Thanks.

Jianghai _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb