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
>>
>
>
|
