This seems to be fixed for sphere refine now which is great (in r6068), but not yet for real space refine zone (e.g. try in the 1G72 case below). Niche case I know, but disulfides on loops are not all that uncommon.
Cheers,
Oliver.
On Fri, 15 Apr 2016 17:39:54 +0100, Oliver Clarke <[log in to unmask]> wrote:
>And actually doesn't seem to be just sphere refine. Real space refine zone exhibits the same behaviour, e.g. check PDB 1G72 Cys6-Cys12 chain B - same results with refine zone or sphere refine, disulfide blows apart.
>
>Cheers,
>Oliver.
>
>On Thu, 14 Apr 2016 14:35:56 -0700, Kevin Jude <[log in to unmask]> wrote:
>
>>I've noticed that sphere refine is sometimes breaking disulfide bonds.
>>This manifests in two ways:
>>
>>the bond is maintained only if I am centered on one of the SG atoms, but
>>not on the other atom or on any other atom in the vicinity
>>
>>the bond is broken no matter where I am centered
>>
>>All of these bonds are defined by SSBOND cards (this structure has been
>>refined with Buster), and the disulfide is supported by the electron
>>density. Sphere refinement of Asn-NAG residues works. I'm using the 0.8.3
>>stable binary from Bill Scott. Is this a bug, or is there something more I
>>should be doing to restrain these links?
>>
>>Best wishes
>>Kevin Jude
>>
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