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) ***************************************************************
