On Wed, 30 May 2012 13:16:12 +0100
Ian Tickle wrote:
> From the point of view of deciding which are the alternate settings I
> don't think it's helpful to consider polar directions anyway. What
> matters is which symmetry axes of the lattice are not present in the
> point group.
Possibly relev
> It does, at least my edition (Vol. A: 5th ed., 2002, Table 10.2.1.2,
> p.806) does - ITC has everything you need to know about space groups
> (and a lot more besides)!
Actually, as the aforementioned table indicates, it's not correct to
talk about "polar and non-polar space groups", but only abo
Hi Ian,
You're right the information is there... but not where I was expecting
it (on the page corresponding to an individual space group). It had
never occurred to me that it could be somewhere else.
So thanks, and regards to Jasmine.
Fred.
Ian Tickle wrote:
Hello Fred
On 30 May 2012 07:
Hello Fred
On 30 May 2012 07:55, Vellieux Frederic wrote:
> Hi there,
> But: trigonal (and hexagonal) space groups "are" (usually?) polar. The cell
> axis "c" can go "up" or can go "down", and in order to get a consistent
> indexing you need to check both indexing systems when you scale additio
Hi Fred,
On Wed, May 30, 2012 at 08:55:35AM +0200, Vellieux Frederic wrote:
> For practical purposes, a "derivative" is considered non isomorphous
> when the differences in unit cell parameters exceed ca. 1% (this is
> because if you take 2 crystals from the same crystallisation drop
> and collect
If the data sets are twinned, large differences between derivatives are to be
expected unless the twin fraction is very, very low (>1-2%). Given the above,
I think nothing can be said until the data are all detwinned - and of course
the correct axial interchange done.
Adrian
On 30 May 2012,
Hi there,
I am not certain that the thread is "P321 space group reindex problem"
any more.
But: trigonal (and hexagonal) space groups "are" (usually?) polar. The
cell axis "c" can go "up" or can go "down", and in order to get a
consistent indexing you need to check both indexing systems whe
Hi,
Le 30/05/2012 08:29, Qixu Cai a écrit :
Thank you for your remind of the twin problem.
It is always a pleasure to be helpful ;-)
By the way, you stated the spacegoup is P321... did you check systematic
absences ? could it be P3121 / P3221 ?
I checked all of the datasets by Xtriage, an
Thank you for your remind of the twin problem.
I checked all of the datasets by Xtriage, and found that the native is not
twinned, but the derivant1 and derivant2 are both twinned.
So is the Rfactor between derivants and native useful for the judgement of
the success of the heavy atom soaking?
Why the 29% Rfactor indicate the derivatives are not isomorphous to native
dataset?
Native dataset cell constant: 181.39 181.39 110.217 90 90 120
derivative1 cell constant: 181.909 181.909 109.62 90 90
120Rfactor to native: 26%
derivative2 cell constant: 181.527 181.527 109.32
Hi,
it is therefore likely that your spacegroup is really P321... hopefully,
your data set is not twinned, did you check that ?
You are left with 2 possible indexing schemes, as already mentionned.
Chek scaling derivative / native scaling for each indexation of the
derivative : the lowest Rf
At first, I processed the data at P3 space group. But after phenix.xtriage
analysis, the Xtriage told me the space group must be P321, so I used P321
to process my data, and got an acceptable Rmerge.
Qixu Cai
2012/5/29 Phil Evans
> How do you know the point group is 321? What does Pointless t
Hi Qixu
Whether it's valid to simply swap h and k depends on whether you have
anomalous data (I assume you don't have any phases at this stage). If
not there's no issue with inverting the hand, but if you do then you
must either remove the anomalous data to avoid confusing yourself and
others lat
How do you know the point group is 321? What does Pointless tell you if you put
in the unmerged data?
Despite some of the things said earlier (by me!), the possible indexing schemes
in 321 are h,k,l and -h,-k,l
If that doesn't work, it suggests that the point group is a lower symmetry eg P3
Phi
Dear all,
thank you for your help.
I think I must describe my case in detail. I collected a native dataset and two
heavy atom derivant datasets （in fact, i don not know whether these two kind of
heavy atom have soked into the crystal, i just collect the data to check it）.
i processed all of th
George
The CCP4 programs (I can't speak for others) involved with isomorphous
replacement, i.e. scaling, FFT for difference Pattersons & Fouriers,
and heavy-atom refinement (e.g. MLPHARE), mostly require that the
native data and that of all the derivatives be not only in the same
a.u. but sorted i
Although there is no need for a "standard" reciprocal asu, it is convenient to
have all your datasets in the same convention when it comes to comparing and
combining different isomorphous datasets (ie to do it once rather than every
time you compare them). It doesn't matter what the "standard" i
Phil,
On 29 May 2012 15:09, Phil Evans wrote:
> No the hand-preserving transformation in 321 is (k,h,-l)
But that's an equivalent of the space group so it won't transform from
the alternate setting (-h, -k, l). It will just give you a _different_
a.u. of the _same_ setting. We need the _same_
Which programs require that the data be the 'standard' a.u.? None of
mine require this.
George
On 05/29/2012 03:44 PM, Ian Tickle wrote:
Mark, thanks for pointing that out, I see it now:
In P321 the only possible alternate indexing is (-h, -k, l): this is a
2-fold || c which is an operator of
As Graeme points out this is the easy way to do this
Pointless will (now) correctly handle anomalous and phase columns in a
reindexing
Phil
On 29 May 2012, at 09:57, Graeme Winter wrote:
> Hello Qixu Cai,
>
> What you want is a reindexing operator which permutes the axes rather
> than one wh
On 29 May 2012, at 15:02, Ian Tickle wrote:
> Phil,
>
> On 29 May 2012 14:08, Phil Evans wrote:
>> NO do NOT invert the hand. If you do you will end up with left-handed
>> helices etc
>
> Surely not if you take care to also change the signs of the anomalous
> differences?
I suppose that's tru
Qixu, yes obviously any sub-group is a possible indexing (all the way
down to P1 !). You need to compare your Rpims etc.
Cheers
-- Ian
On 29 May 2012 15:03, Qixu Cai wrote:
> P3 is another possible alternate indexing? is that correct?
>
>
>
> 2012/5/29 Ian Tickle
>>
>> Mark, thanks for pointi
P3 is another possible alternate indexing? is that correct?
2012/5/29 Ian Tickle
> Mark, thanks for pointing that out, I see it now:
>
> In P321 the only possible alternate indexing is (-h, -k, l): this is a
> 2-fold || c which is an operator of the hexagonal lattice but is not
> an equivalent
Phil,
On 29 May 2012 14:08, Phil Evans wrote:
> NO do NOT invert the hand. If you do you will end up with left-handed helices
> etc
Surely not if you take care to also change the signs of the anomalous
differences?
> The alternative indexing systems all need to preserve the right-handed axis
Mark, thanks for pointing that out, I see it now:
In P321 the only possible alternate indexing is (-h, -k, l): this is a
2-fold || c which is an operator of the hexagonal lattice but is not
an equivalent reflection.
The standard CCP4 a.u. is h = k, l >= 0 or h > k, k >= 0, so for
example (3,2,1)
NO do NOT invert the hand. If you do you will end up with left-handed helices
etc
The alternative indexing systems all need to preserve the right-handed axis
system imposed by the data integration program (eg k,h,-l)
The ONLY time it is valid to invert the hand is if the indexing/integration
p
Thanks for your help.
How to override the warning?
2012/5/29 Mark J van Raaij
> In different datasets of P321 crystals, when you index them separately,
> the hand may be different and you may need to invert it for some. They
> "prohibition" in reindex is really a warning, and can be overridden
Thanks for your help.
How to use CAD to invert the hand?
2012/5/29 Ian Tickle
> In principle there's no reason why you can't invert the hand of the
> indices, as long as the program which does it also takes care to
> convert any hand-dependent columns such as anomalous differences,
> F+/F- etc
In different datasets of P321 crystals, when you index them separately, the
hand may be different and you may need to invert it for some. They
"prohibition" in reindex is really a warning, and can be overridden.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Naciona
In principle there's no reason why you can't invert the hand of the
indices, as long as the program which does it also takes care to
convert any hand-dependent columns such as anomalous differences,
F+/F- etc in the appropriate manner at the same time. The program
will also need to convert any pha
Hello Qixu Cai,
What you want is a reindexing operator which permutes the axes rather
than one which changes the sign of an axis. The easiest way to do this
is with pointless:
pointless hklin input.mtz hklref reference.mtz hklout output.mtz
and let pointless figure out the right operation to use
Hi,
as reindex tells you, if you change h k l to h k -l, you are changing
the hand of your system, which is not allowed.
In P321 group, you only have two possible indexations :
h k l and k h -l (note that h and k are switched).
You have a good explanation on indexation problem on the CCP4 web
Dear all,
I have a dataset at P321 space group. And I want to reindex from (h,k,l)
to (k,h,l) or (h,k,-l), because I want to merge this dataset to the
native dataset.
At first, I used the "reindex" program in CCP4i, and got an error:
(either for (k,h,l) or (h,k,-l))
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