Isn't lowering the symmetry equivalent to using multiple models/conformations for one map? I remember seeing this done with the infamous MSBA structure from a few years ago, so caveat emptor I guess. And further, wouldn't using strict NCS make things equivalent to the higher-symmetry space group? And then violating the NCS in places would then just be equivalent to modelling multiple conformations, no?
JPK On Tue, Mar 19, 2013 at 11:34 AM, Phoebe A. Rice <pr...@uchicago.edu> wrote: > Hi Zbyszek, > If the issue is perfect twinning, I agree - good point! > But you don't want to confuse people who simply have > nearly-but-not-quite crystallographic symmetry (OK, I'm being a bit > pedagogical here, but a lot of newbies read the BB). We had a case of P31 > that was so close to P61 we actually solved the molecular replacement > problem in P61, then expanded it back and re-rigid-bodied it. We've played > similar games with translational pseudo-symmetry (ignoring the weak spots > at first). In cases like that it is important to properly reprocess the > data in the lower symmetry space group (or smaller unit cell) because there > is real information in those small differences. However, the point about > Rfree holds for twinning or rotational pseudo-symmetry: the Rfree flags > should be expanded by the xtal symmetry operators, not re-picked in the > lower symmetry space group. > Phoebe > > ++++++++++++++++++++++++++++++++++++++++++ > > Phoebe A. Rice > Dept. of Biochemistry & Molecular Biology > The University of Chicago > 773 834 1723; pr...@uchicago.edu > http://bmb.bsd.uchicago.edu/Faculty_and_Research/ > http://www.rsc.org/shop/books/2008/9780854042722.asp > > ________________________________________ > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zbyszek > Otwinowski [zbys...@work.swmed.edu] > Sent: Tuesday, March 19, 2013 9:37 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree > > It is a clear-cut case of crystal packing disorder. The tell-tale sign is > that data can be merged in the higher-symmetry lattice, while the number > of molecules in the asymmetric unit (3 in P21) is not divisible by the > higher symmetry factor (2, by going from P21 to P21212). > From my experience, this is more likely a case of order-disorder than > merohedral twinning. The difference between these two is that structure > factors are added for the alternative conformations in the case of > order-disorder, while intensities (structure factors squared) are added in > the case of merohedral twinning. > > Now an important comment on how to proceed in the cases where data can be > merged in a higher symmetry, but the structure needs to be solved in a > lower symmetry due to a disorder. > > !Such data needs to be merged in the higher symmetry,assigned R-free flag, > and THEN expanded to the lower symmetry. Reprocessing the data in a lower > symmetry is an absolutely wrong procedure and it will artificially reduce > R-free, as the new R-free flags will not follow data symmetry! > > Moreover, while this one is likely to be a case of order-disorder, and > these are infrequent, reprocessing the data in a lower symmetry seems to > be frequently abused, essentially in order to reduce R-free. Generally, > when data CAN be merged in a higher symmetry, the only proper procedure in > going to a lower-symmetry structure is by expanding these higher-symmetry > data to a lower symmetry, and not by rescaling and merging the data in a > lower symmetry. > > Zbyszek Otwinowski > > > Dear all, > > We have solved the problem. Data processing in P1 looks better (six > > molecules in ASU), and Zanuda shows a P 1 21 1 symmetry (three molecules > > in > > ASU), Rfactor/Rfree drops to 0.20978/0.25719 in the first round > > of refinement (without put waters, ligands, etc.). > > > > Indeed, there were one more molecule in ASU, but the over-merged data in > > an orthorhombic lattice hid the correct solution. > > > > Thank you very much for all your suggestions, they were very important to > > solve this problem. > > > > Cheers, > > > > Andrey > > > > 2013/3/15 Andrey Nascimento <andreynascime...@gmail.com> > > > >> *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* > >> > > > > > Zbyszek Otwinowski > UT Southwestern Medical Center at Dallas > 5323 Harry Hines Blvd. > Dallas, TX 75390-8816 > Tel. 214-645-6385 > Fax. 214-645-6353 > -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************
