Dear Rafal,
The difference map you show in your attachment has an echo of the main structure sort of look. So, I suggest you examine your diffraction images specifically looking out for a supercell of weak intensity spots, not picked up by the autoindexing, between the main lattice of intensities, which provided your current unit cell.
Best wishes,
John
Emeritus Professor John R Helliwell DSc
> On 29 Jul 2020, at 13:42, Rafal Dolot <[log in to unmask]> wrote:
>
> Dear CCP4 users,
>
> I'm working on the another nucleic acid duplex structure. After several stages of rebuilding and refinement I observed something like a "shadow" of the second duplex position. Have you any ideas to explain this phenomena? Should I place the second molecule with occupancy completed to the first one? Or maybe is it a kind of disorder in crystal lattice? Data were collected to 1.02A using synchrotron radiation (processed with XDS), but I have another datasets collected to lower resolution (from Zn-SAD) with visible similar effects. Refinement was done using Refmac (R/Rfree 21.5/24.0). Data not appeared to be twinned, but Xtriage detected pseudo-translational symmetry.
>
> Thank you for any advices.
>
> Rafal
>
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> |Rafal Dolot, Ph.D. |
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> |Polish Academy of Sciences |
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