[phenixbb] Phenix.refine generates new bond between SO4 and OH of glycerol
Pavel Afonine
pafonine at lbl.gov
Thu Jul 28 17:52:07 PDT 2016
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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