Well - there s nothing there to indicate twinning, although as you say
it is hard to be sure with a pseudo translation...
The contrast doesnt look brilliant, but then it often doesnt..
What about phaser? If it gives a contrast between one spacegroup and the
others I always think that is a good sign..
It will take a while though..
Eleanor
Phil Evans program othercell suggests you could reindex to get two axes
equal.. And that is a prequisite for twinning .
C 1 2/m 1 192.3 192.3 117.2 90.0 90.0 92.0 1.98 [k-l,k+l,h]
Same cell
[-k+l,-k-l,h]
Eleanor
Kay Diederichs wrote:
Eleanor Dodson schrieb:
You dont mention any twinning tests?
sorry, I forgot to mention that the twinning tests do not show twinning.
Rather, the actual curves in the "Cumulative distribution of H" lie on
the "not-twinned-at-all" (i.e opposite) side of the alpha=0 curve (see
plot below). But I'm pretty sure that this is due to the
pseudo-translation (almost centering) which results in a high
proportion of very weak reflections - contrary to what you get with
twinning.
That's what I get from sfcheck, when run in P212121:
Perfect twinning test <I^2>/<I>^2 : 3.1699
Partial Twinning test:
-h,+l,+k
Polar angles: 135.00 -89.99 179.99
Alpha(twin fraction),Npair,Ior,Tol :-0.109 162588 2 0.030
--- Partial Twinning Test : H = !I(h1)-I(h2)!/(I(h1)+I(h2)) ---
Alpha(twinning fraction) = 1/2 - <H>
Reflection related to hkl :
-h,+l,+k
Cumulative distribution of H
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
*---+---+---+---+---+---+---+---+---+---+
O+++.+ . . . . . . . . !
O ++.+ . + . . . . . . . !
!O +++ + . +. . . . . . !
0.10!-O-++-+--+---------+-------------------!
! O .++ + .+ . . .+ . . . !
! O. + + + . +. . . . + . . !
! O +.+ + . + . . . . +. !
0.20!---O---+-+--+------+-------------------+ alpha=0.4
! .O .+ +. +. . +. . . . +
! . O . + + .+ . .+ . . . +
! . O . +. + . + . . + . . +
0.30!------O----+--+----+---------+---------+
! . O .+ + . + . . .+ . +
! . O . + .+ . +. . . +. +
! . .O . +. +. .+ . . . + +
0.40!---------O-----+---+------+------------+ alpha=0.3
! . . O. .+ .+ . + . . +
! . . O. . + . +. . + . . +
! . . O . +. + . + . +
0.50!------------O------+----+-------+------+
! . . .O . .+ . + . . +. +
! . . . O . . + . + . .+ +
! . . . O. . +. .+ . . + +
0.60!---------------O-------+-----+---------+ alpha=0.2
! . . . .O . .+ . +. . +
! . . . . O . . + . .+ . +
! . . . . O. . +. . + . +
0.70!------------------O--------+------+----+
! . . . . O . .+ . + +
! . . . . .O . . + . .+ +
! . . . . . O. . +. . ++
0.80!-----------------------O-------+-------+ alpha=0.1
! . . . . . .O . .+ . +
! . . . . . . O . . + . +
! . . . . . . O. . +. +
0.90!----------------------------O------+---+
! . . . . . . . O. .+ +
! . . . . . . . .O . + +
! . . . . . . . . O. ++
H *---+---+---+---+---+---+---+---+---+---* alpha=0
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Of course this plot looks _very_ different if I run it in P1 because
then sfcheck uses -h,k,-l as twinning operator - it then looks like
perfect twinning.
The L test, now part of the newest ctruncate is pretty good at
detecting twinning even with the NCS translation.
this is the L test from ctruncate 1.0.0 : 30/10/08 run in P212121 :
$TABLE: L test for twinning:
$GRAPHS: cumulative distribution function for |L|:0|1x0|1:1,2,3,4:
$$ |L| Observed Expected_untwinned Expected_twinned $$
$$
0.000000 0.000000 0.000000 0.000000
0.050000 0.048142 0.050000 0.074938
0.100000 0.093721 0.100000 0.149500
0.150000 0.139205 0.150000 0.223312
0.200000 0.184799 0.200000 0.296000
0.250000 0.230867 0.250000 0.367188
0.300000 0.277173 0.300000 0.436500
0.350000 0.323650 0.350000 0.503563
0.400000 0.370747 0.400000 0.568000
0.450000 0.418233 0.450000 0.629437
0.500000 0.466569 0.500000 0.687500
0.550000 0.515615 0.550000 0.741812
0.600000 0.565706 0.600000 0.792000
0.650000 0.616860 0.650000 0.837688
0.700000 0.669232 0.700000 0.878500
0.750000 0.723200 0.750000 0.914062
0.800000 0.779144 0.800000 0.944000
0.850000 0.836994 0.850000 0.967938
0.900000 0.896933 0.900000 0.985500
0.950000 0.957486 0.950000 0.996313
1.000000 1.000000 1.000000 1.000000
$$
And SFCHECK does a good job too.
If these are inconclusive I would not assume twinning.
Usually you can get solutions for MR with twinned data, but I havent
much experience of the signal quality..
Can you solve it in P1 then sort out the spacegroup later?
I tried; this is the full story:
I ran molrep (version 10.2.12 from CCP4 6.1.0) in P1, with NMON=8. It
uses the pseudo-translation vector and thus places 4 times 2
molecules. In the "fast" mode (standard RF and TF without rigid body
refinement) the "contrast" is 1.93/1.77/1.87/14.72 for the
1st/2nd/3rd/4th pair of molecules. However the result is different if
I run it in "medium" (contrast=2.82/4.56/1.55/3.10) or "slow"
(2.87/11.47/2.01/2.59) mode, and molrep only writes out 4 molecules
instead of 8, in these two modes.
I therefore suspected a bug and upgraded to molrep 10.2.27 from
Alexei's webpage. But this version does not find the 8 molecules any
more:
Corr_for_fixed_model: 0.166
WARNING: program can not improve current model
result is "molrep.crd" with 4 monomers
so this is quite confusing.
I calculated structure factors from the P1 arrangement that I got in
"fast" mode, from the 10.2.12 version. But it clearly is
non-orthorhombic, and should have tetartohedral twinning to account
for the pseudo-orthorhombic data.
This is where I stopped and thought about asking on CCP4BB.
best,
Kay
Eleanor
Kay Diederichs wrote:
Dear all,
we have crystals that nicely diffract to 1.7 A (sharp spots), with
the following characteristics and findings:
a) the data appear as P212121, with axes 117.2 133.6 138.3 (if
reduced in P1, the largest deviation of any angle from 90° is 0.2°);
the odd screw-axis reflections are mostly indistinguishable from
noise; the data do not scale significantly better in P2/P21 (any
setting) or P1.
b) there is a good model available, with coords known from a complex
of this protein with another one; two molecules of this model would
give 64% solvent in P212121 which appears reasonable for a membrane
protein
c) the structure cannot be solved with this model in P212121, nor
can it be solved in P222, P2122, P2212, P2221, P21212, P22121, P21221
d) we conclude that the true space group must be P2 or P21 (with one
of the three possible settings), with almost-perfect twinning. Or it
is P1 with tetartohedral twinning. There are thus still six + one
possibilities.
e) MOLREP tells us
--- Check Patterson for pseudo-translation ---
PST_limit : 0.125 of origin peak
INFO: pseudo-translation was detected.
Origin Patterson peak: P,P/sig : 57.748 257.690
1 Patterson. peak : p,P/sig : 28.773 128.395
2 Patterson peak : P,P/sig : 16.551 73.856
3 Patterson peak : P,P/sig : 8.502 37.936
Peak 1: trans.vector /ort/ : 0.011 55.688 69.399
trans.vector /frac/: 0.000 0.416 0.500
Peak 2: trans.vector /ort/ : 58.554 66.863 0.000
trans.vector /frac/: 0.500 0.500 0.000
Peak 3: trans.vector /ort/ : 58.565 11.385 69.399
trans.vector /frac/: 0.500 0.085 0.500
INFO: translation vector of peak 1 will be used.
Two molecules (for the orthorhombic spacegroups) may produce only
one pseudo-translation vector. As there is more than one strong
pseudo-translation vector, I conclude that we have at least 3
molecules in the ASU (consistent with monoclinic).
f) we've calculated all seven molecular replacement searches of d)
in MOLREP. The contrast is very high in all cases. However, Refmac
rigid-body refinement of the solutions, with "Twin refinement"
activated, gives about 51% R and the same for Rfree (give or take 1
%), in all cases.
I'm wondering: how reliable is a rotation search in the presence of
perfect twinning? Is there any molecular replacement program that
can take a given twinning operator into account in the rotation and
translation search?
Any other hints what to try?
best,
Kay
