Or give it to arp/warp, either with the current model to improve or with phases
from the current model to build new model?
Phoebe A. Rice wrote:
> What happens if you solvent-flatten/flip/massage that map, but tell the software the solvent content much lower than
> what you think it is now? Maybe you'll find another copy of the molecule?
>
> ------------------------------------------------------------------------------------------------------------------------
> *From:* CCP4 bulletin board [[log in to unmask]] on behalf of Andrey Nascimento [[log in to unmask]]
> *Sent:* Friday, March 15, 2013 1:39 PM
> *To:* [log in to unmask]
> *Subject:* [ccp4bb] Strange density in solvent channel and high Rfree
>
> *Dear all,*
>
> *I have collected a good quality dataset of a protein with 64% of solvent in P 2 21 21 space group at 1.7A resolution
> with good statistical parameters (values for last shell: Rmerge=0.202; I/Isig.=4.4; Complet.=93% Redun.=2.4, the overall
> values are better than last shell). The structure solution with molecular replacement goes well, the map quality at the
> protein chain is very good, but in the final of refinement, after addition of a lot of waters and other solvent
> molecules, TLS refinement, etc. ... the Rfree is a quite high yet, considering this resolution (1.77A).(Rfree= 0.29966
> and Rfactor= 0.25534). Moreover, I reprocess the data in a lower symmetry space group (P21), but I got the same problem,
> and I tried all possible space groups for P222, but with other screw axis I can not even solve the structure.*
>
> *A strange thing in the structure are the large solvent channels with a lot of electron density positive peaks!? I
> usually did not see too many peaks in the solvent channel like this. This peaks are the only reason for these high R's
> in refinement that I can find. But, why are there too many peaks in the solvent channel???*
>
> *I put a .pdf file (ccp4bb_maps.pdf) with some more information and map figures in this link:
> https://dl.dropbox.com/u/16221126/ccp4bb_maps.pdf*
>
> *
> *
>
> *Do someone have an explanation or solution for this?*
>
> **
>
> *Cheers,*
>
> *Andrey*
>
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