[phenixbb] Phenix.refine generates new bond between SO4 and OH of glycerol

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jul 29 06:37:23 PDT 2016


Please send me the file directly.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
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

On Thu, Jul 28, 2016 at 5:52 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi,
>
>
> sounds like a bug. Could you please send me PDB file (please send to me
> directly, not entire mailing list)?
>
>
> Meanwhile, a quick work-around is to use link_ligands=False (if you are
> using command line) or if using the GUI:
>
>
> Refinement settings -> Automatic linking options -> uncheck "Link ligands
> to protein" .
>
>
> Pavel
>
>
>
> On 7/28/16 05:39, Amber Lee wrote:
>
> Dear all, Dear Pavel,
>
>
> I have encountered a problem where a new bond was generated between the O
> of SO4 and O(H) of my ligand (with a glycerol head group, I call it
> glycerol here).
>
>
> As shown in the figure in the Dropbox link below, I have placed the
> glycerol (purple) in the density and it fits well. The distance between the
> O of SO4 and the OH of glycerol was 2.55 angstrom. After refinement
> (yellow) however, the glycerol was pulled out of density with the distance
> changed to 1.27 angstrom, therefore forming a new bond.
>
>
> When hydrogens were added to the glycerol, the glycerol was again pulled,
> forming a C-O bond between SO4 and glycerol.
>
>
> When the positions (xyz) of the glycerol atoms were fixed, the SO4 was
> pulled towards glycerol, making a O-O bond between SO4 and glycerol.
>
>
> When the positions of the SO4 and glycerol were both fixed during the
> refinement, the result came out saying the bond length was too long between
> the the O (SO4) and the O (glycerol).
>
>
> Thus I thought Phenix must treated it as a covalent bond.
>
>
> I have tried Rafmac and it did not do this to the model. The cif files etc
> were the same for Phenix and Rafmac.
>
>
> The problem appeared both on version 1.10-2152 and the latest version
> 1.10.2155.
>
>
> How could I fix this problem?
>
>
> Many thanks,
>
>
> Jingyi Hu
>
>
>
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