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

[Pavel Afonine]

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
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160728/4876fb00/attachment.htm>