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

[Pavel Afonine]

Nigel,

I have the file.

Pavel


On 7/29/16 06:37, Nigel Moriarty wrote:
> 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 <http://CCI.LBL.gov>
>
> On Thu, Jul 28, 2016 at 5:52 PM, Pavel Afonine <pafonine at lbl.gov 
> <mailto: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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