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Dear Napo,
to illustrate Felix Frolow's comment, take Solution-1 and the new data
to refmac5 and run 'rigid body refinement'. I would not be surprised if
you get a reasonable map with nearly the same R/Rfree as your MR
solution, which means that this solution and the one from MR are
equivalent (because of the freedom of choice for the origin some space
groups allow you).
Tim
On 11/20/2011 06:42 AM, Napolećo Valadares wrote:
> Hello,
> I'm observing a very strange phenomena (at least to me, I'm a beginner).
> It is related to symmetry (I think).
>
> I got a data set at 1.95A (I/Sigma 3.5, R-Factor and R-meas < 35% in the
> last shell) and a partially refined solution with R/Rfree 22/24, 166
> aminoacids observed and around 30 solvent molecules. I'll call this
> Solution-1. The refinement was smooth, the densities were very clearly
> "asking" for the correct missing side chains and the map looks good.
>
> The space group I'm using is P212121, pointless and XDS agree with that
> (but me and pointless both have a long history of being wrong about
> space groups). Phenix.xtriage says there's no twinning.
>
> I took Solution-1 and used it as a template in a molecular replacement
> in the same space group (P212121) using the same mtz as the one used to
> refine the template. I got a different (not superposed in space)
> solution (called Solution-2, scores by Phaser RFZ=24.2 TFZ=33.0 PAK=0
> LLG=1413 LLG=1899) that was readily refined in Phenix to R/Rfree 24/26
> without any solvent molecule.
>
> - The solutions are not superposed in space, although they are
> near-identical and can be superposed yielding a C-alpha rmd =0.001.
> - Both structures present VERY similar density maps. The maps are not
> superposed in space, but when you "run the chain" in one map in Coot and
> do the same in the other it they the present exactly the same features.
> It is impossible to ignore their similarities.
> - Both structures and maps present the same origin and unit cell.
> - If I add to Solution-2 the equivalent solvent molecules of Solution-1
> (I did this by superposing Solution-1 to Solution-2 then copy/pasting
> the solvent molecules), the R/Rfree become 22/24. This is a clear
> indication that the solutions are related.
> - I can't find any MR solutions using the same template and space groups
> P222, P2221 and P21212.
>
> How two different sets of phases can yield maps with the same features?
> What is happening, wrong space group? I have a feeling my lack of
> experience is the problem.
> Thank you.
> Regards,
> Napo
>
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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