God bess the symmetry, we are saved from the over-interpreting symmetry (except probably of very exotic cases) by the very high Rsym factors around 40% 50% if the symmetry is wrong. Even wild rejection of outliers, cannot reform "acceptable" Rmerge. In my personal repository, 1QZV is a manifest of that. In 4.4 angstrom resolution, wrong interpretation of 90.2 angle monoclinic angle as 90 degrees orthorhombic supported by two molecules in the monoclinic asymmetric was corrected in the middle of the first data collection. Habitual on-fly processing of the data (integration and repetitive scaling after every several frames with HKL) detected that about half-through the data R factor in orthorhombic space group jumped to 40% from about 7%. Reindexing solved the problem on the spot. I still keep the raw data. Needless to say that before about a decade we would make precession photographs (I still own precession camera) and would not make such a mistake. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 3, 2011, at 21:42, Clemens Vonrhein wrote: Hi James, scary ... I was just looking at exactly the same thing (P21 with beta~90), using the same tool (POINTLESS). Currently I'm going through the structures for which images can be found ... I haven't gone far through that list yet (in fact actually only the first one), but this first case should indeed be in a higher spacegroup (P 2 21 21). As you say (and that's what Graeme looks for): finding 'over-merged' datasets can be a bit more tricky ... once the damage is done. I have the hunch that it might happen even more often though: we tend to look for the highest symmetry that still gives a good indexing score, right? Otherwise we would all go for P1 ... Some other interesting groups for under-merging: * orthorhombic with a==b or a==c or b==c (maybe tetragonal?) * trigonal (P 3 etc) when it should be P 6 * monoclinic with beta==120 A few cases for each of those too ... all easy to check in ftp://ftp.wwpdb.org/pub/pdb/derived_data/index/crystal.idx and then (if structure factors are deposited) running POINTLESS on it (great program Phil!). Cheers Clemens On Thu, Nov 03, 2011 at 12:00:33PM -0700, James Holton wrote: I tried looking for such "evil symmetry problem" examples some time ago, only to find that primitive monoclinic with a 90-degree beta angle is much more rare than one might think by looking at the PDB. About 1/3 of them are in the wrong space group. Indeed, there are at least 366 PDB entries that claim "P2-ish", but POINTLESS thinks the space group of the deposited data is higher (PG222, C2, P6, etc.). Now, POINTLESS can be fooled by twinned data, but at least 286 of these entries do not mention twinning. Of these, 40 explicitly list NCS operators (not sure if the others used NCS?), and 35 of those were both solved by molecular replacement an explicitly say the free-R set was picked at random. These are: Now, I'm sure there is an explanation for each and every one of these. But in the hands of a novice, such cases could easily result in a completely wrong structure giving a perfectly reasonable Rfree. This would happen if you started with, say, a wrong MR solution, but picked your random Rfree set in PG2 and then applied "NCS". Then each of your "free" hkls would actually be NCS-restrained to be the same as a member of the working set. However, I'm sure everyone who reads the CCP4BB already knew that. Perhaps because a discerning peer-reviewer, PDB annotator or some clever feature in our modern bullet-proof crystallographic software caught such a mistake for them. (Ahem) Of course, what Graeme is asking for is the opposite of this: data that would appear as "nearly" PG222, but was actually lower symmetry. Unfortunately, there is no way to identify such cases from deposited Fs alone, as they will have been overmerged. In fact, I did once see a talk where someone managed to hammer an NCS 7-fold into a crystallographic 2-fold by doing some aggressive "outlier rejection" in scaling. Can't remember if that ever got published... -James Holton MAD Scientist On 11/2/2011 1:33 AM, Graeme Winter wrote: Hi Ed, Ok, I'll bite: I would be very interested to see any data sets which initially were thought to be e.g. PG222 and scale OK ish with that but turn out in hindsight to be say PG2. Trying to automatically spot this or at least warn inside xia2 would be really handy. Any pseudosymmetric examples interesting. Also any which are pseudocentred - index OK in C2 (say) but should really be P2 (with the same cell) as the "missing" reflections are in fact present but are just rather weaker due to NCS. I have one example of each from the JCSG but more would be great, especially in cases where the structure was solved& deposited. There we go. Now the matter of actually getting these here is slightly harder but if anyone has an example I will work something out. Please get in touch off-list... I will respond to the BB in a week or so to feed back on how responses to this go :o) Best wishes, Graeme -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
