[phenixbb] Refinement

Nigel Moriarty nwmoriarty at lbl.gov
Tue May 26 13:49:10 PDT 2015

On Mon, May 25, 2015 at 2:35 AM, mohamed noor <mohamed.noor34 at gmail.com>

> was referring to the partial charge in the restraint file, which IMHO
> should be translated to the model.

The PDB file format is for formal integer charges. The partial charges will
simply not fit.

> I have a second problem - I'm using the cif file for refinement but the
> angles and bond lengths still get distorted. These are flagged as outliers
> in phenix.refine. Why is it not using the values that I input? My
> resolution is 3.8 A, but I still end up with positive density around all
> the hemes. In fact, the problems with hemes are the cause of a large
> majority of my outliers. I did a parallel refinement with and without the
> restraint file - it doesn't make any difference.

Please send the final model and .geo file directly off-list.



Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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