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
