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
120 Rfactor to native: 26%
derivative2 cell constant: 181.527 181.527 109.32 90 90
120 Rfactor to native: 29%
The Rfactor at low resolution is larger than in high resolution.
Could you please to help me figure out where the heavy atoms had been
soaked into the crystal?
Thank you very much.
Best wishe,
Qixu Cai
2012/5/30 Laurent Maveyraud <laurent.maveyr...@ipbs.fr
<mailto:laurent.maveyr...@ipbs.fr>>
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 Rfactor will likely
indicate the right one.
It appears that you end up with Rfactor of about 29 %, which
suggest that your derivatives are not isomorphous to your native
dataset. How do cell parameters compare for each data set ?
Check also how the Rfactor varies with resolution, you might still
have usefull phasing info at low resolution.
hope this helps
laurent
Le 30/05/2012 07:50, Qixu Cai a écrit :
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 <p...@mrc-lmb.cam.ac.uk
<mailto:p...@mrc-lmb.cam.ac.uk> <mailto:p...@mrc-lmb.cam.ac.uk
<mailto:p...@mrc-lmb.cam.ac.uk>>>
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
Phil
On 29 May 2012, at 16:29, Qixu Cai wrote:
> 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 three datasets with automar, and
merged them
by CAD. I used scaleit to get the Rfactor between datasets
and got a
strange result. the R factor between derivant1 and native
is 26% and
the R factor between derivant2 and native is 59%!
>
> so I think it may be the problem of index （space group is
P321）. so i exchange the h and k of derivant2 by the some awk
script and merged to native data by CAD. After scaleit
analysis, I
got the R factor 29% between derivant2 and native.
>
> Here is my questions,
>
> 1, at my case, is that right to invert the hand? is that the
special problem of the P3 or p321 space group?
>
> 2, I have carryed out some suggestion of yours, such as use
pointless （use native data as reference for derivant2
reindex）, or
reindex the derivant2 dataset by （k, h, -l）, and I always
got the
high R factor 59% between derivant2 and native.
>
> Any suggestion?
>
> thanks a lot!
>
> Qixu Cai
>
>
> 在 2012-5-29，下午10:36，Laurent Maveyraud
<laurent.maveyr...@ipbs.fr
<mailto:laurent.maveyr...@ipbs.fr>
<mailto:laurent.maveyr...@ipbs.fr
<mailto:laurent.maveyr...@ipbs.fr>>> 写道：
>
>> Hi... and apologies !
>>
>> I was a little quick in my answer... in P321, h k l and
-h -k l
are valid indexing schemes...
>> It is in P3 that you can have h k l and k h -l
>> as Ian and Phil agreed on the BB !
>>
>> sorry,
>> laurent
>>
>> Hi,
>>
>> you might have several possible spacegroups possible when
processing your data (at the indexation step). These will
be based
on the metrics of your cell (vector length and angles). If you
happen to have something like a = b, and alpha=beta90° and
gamma=120°, then it is likely that your crystal is trigonal or
hexagonal.
>>
>> You will have to wait until the scaling step (or
pointless after
integration) in order to decide which spacegroup is the
right one,
based on the symmetry operations in your dataset and on
systematic
absences. There you have to choose between P3, P31, P32,
P312, P321
in trigonal.
>>
>> When comparing two datasets from trigonal crystals,
even for
identical crystals and hence identical spacegroups, you have
different ways to index your dataset...
>> In P321, one dataset might be indexed one way (eg. h k
l), the
other might be index the other way (k h -l). When you
compared this
two dataset, they will appear to be different, because both
indexing
schemes, although valid, are not equivalent.
>>
>> Take one reflection; e.g. 3 2 1 from your crystal A.
The very
same reflection will be indexed 2 3 -1 for your crystal B,
and the
one indexed 3 2 1 for crytal B will not be equivalent to
the 3 2 1
reflection from crystal A.
>> If you try to merge your two datasets, you will have huge
Rmerge, because you are trying to average non equivalent
reflections.
>>
>> You will have to ensure that the same indexing scheme
is used
for both datasets, eg reindex B using the reindex k h -l
command in
reindex, before being able to merge A and B.
>>
>> hope this helps... please feel free to as if I am not
clear...
>>
>> best regards
>>
>> laurent
>>
>> Le 29/05/2012 16:03, Qixu Cai a écrit :
>>> P3 is another possible alternate indexing? is that
correct?
>>>
>>>
>>> 2012/5/29 Ian Tickle <ianj...@gmail.com
<mailto:ianj...@gmail.com>
<mailto:ianj...@gmail.com <mailto:ianj...@gmail.com>>
<mailto:ianj...@gmail.com <mailto:ianj...@gmail.com>
<mailto:ianj...@gmail.com <mailto:ianj...@gmail.com>>>>
>>>
>>> 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) would be in the standard a.u. (3 > 2
and 2 >=
0). In
>>> the alternate indexing this would be (-3, -2, 1);
however it's
>>> impossible to transform this to the a.u. with any
non-inverting
>>> equivalent. The only possibility is to invert the
hand, i.e.
to (3,
>>> 2, -1) which is again in the a.u..
>>>
>>> So the required re-indexing operator to match (3, 2,
-1) with
(3, 2,
>>> 1) is (h, k, -l) which reindex won't allow without
the LEFT
keyword
>>> (and you would be well-advised to avoid doing it
with phase
columns!).
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>> On 29 May 2012 12:55, Mark J van Raaij
<mjvanra...@cnb.csic.es <mailto:mjvanra...@cnb.csic.es>
<mailto:mjvanra...@cnb.csic.es <mailto:mjvanra...@cnb.csic.es>>
>>> <mailto:mjvanra...@cnb.csic.es
<mailto:mjvanra...@cnb.csic.es>
<mailto:mjvanra...@cnb.csic.es
<mailto:mjvanra...@cnb.csic.es>>>> wrote:
>>>> 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 Nacional de Biotecnologia - CSIC
>>>> c/Darwin 3
>>>> E-28049 Madrid, Spain
>>>> tel. (+34) 91 585 4616
>>>> http://www.cnb.csic.es/~mjvanraaij
<http://www.cnb.csic.es/%7Emjvanraaij>
<http://www.cnb.csic.es/%7Emjvanraaij>
>>> <http://www.cnb.csic.es/%7Emjvanraaij>
>>>>
>>>>
>>>>
>>>> On 29 May 2012, at 13:52, Ian Tickle wrote:
>>>>
>>>>> 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 phase or phase-coefficient
>>> columns, but
>>>>> it will have to do this anyway, even if the hand is not
inverted, in
>>>>> those cases where the space group contains screw
axes (since
>>> then you
>>>>> will get phase shifts on reindexing for certain
subsets of
>>>>> reflections).
>>>>>
>>>>> So if the data consist only of I's or F's without
anomalous
data or
>>>>> phases then inverting the hand will have absolutely
no effect
(it's
>>>>> called "Friedel's Law").
>>>>>
>>>>> I note from the documentation that reindex will
invert the hand
>>> if the
>>>>> keyword 'LEFT' is supplied, though whether it then
treats the
>>>>> anomalous data and phases correctly is anyone's guess!
>>>>>
>>>>> The question is really whether it's likely ever to be
_necessary_ to
>>>>> invert the hand; this will depend on the reciprocal
space
asymmetric
>>>>> unit chosen by the processing program. One could
imagine a
>>> situation
>>>>> where the a.u. chosen by one processing program was on a
different
>>>>> hand from the a.u. required by another. In such a
situation you
>>> would
>>>>> have no choice but to invert the hand of the
indices, though I
>>> suspect
>>>>> you would be better off doing it with CAD which will
do it
reliably,
>>>>> rather than reindex which may not (judging by the
comments in the
>>>>> reindex code!). Whether such a situation ever occurs in
practice, I
>>>>> don't know, maybe not.
>>>>>
>>>>> Cheers
>>>>>
>>>>> -- Ian
>>>>>
>>>>> On 29 May 2012 09:57, Graeme Winter
<graeme.win...@gmail.com <mailto:graeme.win...@gmail.com>
<mailto:graeme.win...@gmail.com
<mailto:graeme.win...@gmail.com>>
>>> <mailto:graeme.win...@gmail.com
<mailto:graeme.win...@gmail.com>
<mailto:graeme.win...@gmail.com
<mailto:graeme.win...@gmail.com>>>> wrote:
>>>>>> 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. You
>>> may find
>>>>>> the following helpful:
>>>>>>
>>>>>> http://www.ccp4.ac.uk/html/reindexing.html
>>>>>>
>>>>>> Best wishes,
>>>>>>
>>>>>> Graeme
>>>>>>
>>>>>> On 29 May 2012 09:48, Qixu Cai <caiq...@gmail.com
<mailto:caiq...@gmail.com>
<mailto:caiq...@gmail.com <mailto:caiq...@gmail.com>>
>>> <mailto:caiq...@gmail.com <mailto:caiq...@gmail.com>
<mailto:caiq...@gmail.com <mailto:caiq...@gmail.com>>>> wrote:
>>>>>>> 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))
>>>>>>>
>>>>>>> ================================================
>>>>>>> Data line--- reindex HKL h, k, -l
>>>>>>> Data line--- end
>>>>>>>
>>>>>>> $TEXT:Warning: $$ comment $$
>>>>>>> WARNING: !!!! Reindexing matrix INVERTS hand !!!!
>>>>>>> $$
>>>>>>> REINDEX: !!!! You are NOT allowed to do this -
Changing
>>> all signs in
>>>>>>> reindexing matrix
>>>>>>> Times: User: 0.0s System: 0.0s Elapsed:
0:00
>>>>>>> =================================================
>>>>>>>
>>>>>>> Could you please tell me the reason?
>>>>>>>
>>>>>>> At last, I converted the mtz file to CNS format,
and write a
>>> script to
>>>>>>> exchange the h and k, and converted to mtz file.
>>>>>>> When I tried to use "cad" to merge this dataset to
the native
>>> dataset, if I
>>>>>>> chose "Automatically check and enforce consistent
indexing
>>> between different
>>>>>>> files",
>>>>>>> the index would be changed back to the original
index. Why?
>>>>>>>
>>>>>>> Thank you very much for your attention.
>>>>>>>
>>>>>>> Best wishes,
>>>>>>>
>>>>>>> Qixu Cai
>>>
>>>
>>
>> --
>> ----------------------------------------------------------
>> Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
>> Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089
>> PICT -- Plateforme Intégrée de Criblage de Toulouse
>> Département Biologie Structurale et Biophysique
>> BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE
>> Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994
>> ----------------------------------------------------------
>>
--
----------------------------------------------------------
Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089
PICT -- Plateforme Intégrée de Criblage de Toulouse
Département Biologie Structurale et Biophysique
BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE
Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994
----------------------------------------------------------
