First spacegrouop - trigonal spacegroups can also be indexed as C2 so it isnt so surprising that a P6/mmm should masquerade as C2. I would look very carefull at the POINTLESS symmetry scores and see if some are more convincing than others.
But how I hate RNA & DNA - molecular replacement struggles because often the molecules pack to form a pseudo-continuous chain so it is easy when searching with one copy to finish up a residue or so out of register.. Do the B factors give you a clue about error? And with only 3A data it will be hard to check the base identities.. Maybe set base occupancies to 0.00 one at a time , refine then see what you see in the difference map. Maybe you might detect a possible different interpretation.... Eleanor On Tue, 8 Jun 2021 at 16:28, CRAIG A BINGMAN < 000021371e2fba31-dmarc-requ...@jiscmail.ac.uk> wrote: > It’s difficult to tell exactly what is happening from your description and > the attached image. Both your description and the image are OK. It’s just > that there are a lot of ways for things to go off the rails. > > Are the molecules stacked end-to-end? In that case, you may have an > incommensurate structure where the molecule is disordered around a > pseudo-continuous helical axis running through the crystal. > > But from this view, it looks like at least two bases are swung out to the > left. I’d omit the interaction region, refine what you can model well as > well as you can, and see if the maps for this region clear up. Keep in mind > that your model might be out of register, so look at the shapes of the > bases carefully to see if you need adjust that. > > On Jun 8, 2021, at 10:14 AM, maps.fa...@gmail.com wrote: > > Hello everyone, > > I am working with an RNA-only structure, data are at 3 Angstroms, and at > first, I thought was in the C2 space group (with 6 molecules in the AU). > > I can't finish building! it, because the structure seems to get in the way > of its neighbor symmetrically! See the attached picture, please! The only 4 > residues that the structure is missing "have to go there", where one > structure meets the other one. The R factors for this spacegroup are around > 0.3. > > However, Phenix Xtriage suggests the symmetry may be higher. So I reindex > in P622, do MR with Phaser (trying all possible space groups in that point > group), and it finds a unique solution in space group P 65 2 2 with TFZ of > 50 and LLG >3000. Of course, the problem persists (one molecule sort of > interfering with the neighbor), not only that but also the refinement > R-factors are substantially higher, 0.37. > > I have to say that the refinement maps look better when I am working with > the C2 spacegroup. I can't understand, though, what is happening at that > "supposedly interface" between the two molecules. Has anybody experienced > anything like this in the past? Can it be a twin? Is it something else? > and... how to fix it? > > Thank you very much in advance. > > Best wishes, > > Almudena > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <Screenshot 2021-06-08 at 16.42.54.png><Screenshot 2021-06-08 at > 16.43.21.png><Screenshot 2021-06-08 at 16.43.38.png> > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
