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))
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
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
Dear all,
Sorry for the question from MAD beginner.
When we process the MAD datasets, including the peak-data, edge-data and
remote-data, which datasets need to be process with anomalous?
I know peak-data obviously need data processing with anomalous, but what
about edge-data and remote-data
Hi,
when processing MAD data, all wavelength should be processed without
enforcing the Friedel's law... If you look at your fluorescence
spectrum, you will see that you have anomalous signal for the peak
(obviously) for the high energy remote and even forh the inflexion point.
For example, i
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Dear Qixu Cai,
MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl)
with I(-h-k-l), both within one data set and between data sets.
Therefore you might get better results if your integration program does
not assume Friedel-pairs to hav
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
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
Dear CCP4BB users,
we would hereby like to introduce XDSAPP, a GUI for the easy and
convenient processing of diffraction data sets using XDS (see also
Krug et al. (2012). J. Appl. Cryst. 45, 568-572).
XDSAPP automates the data processing, generates plots of various
data set statistics and produce
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
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
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
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)
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
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
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
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
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
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
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_
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
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
Hi Mike.
I would be more careful about "incorrect" space group. Yes, sometimes
auto-indexing gives strange results.
However, in your case two sets of crystals differ by two factors, diffraction
quality and space group.
Therefore it seems more likely that you have two crystal forms.
Could you ple
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
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
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
Dear all,
This is Barbara Medagli, working in the structural biology
lab in Italy
Surfing in the molecular dimensions web site
I found this two screens: MIDAS and ProPlex.
I was thinking in buy them as I have to order other
items to this company
Some of you already used those kits?
Any experienc
Dear all,
I need help with finding water in my protein structure using Coot.
I tried to find water with peaks above 1.6 sigma for both the 2Fo-Fc and
mFo-DFc maps.
The result were 253 water molecules found for 2Fo-Fc map and 563 water
molecules found for mFo-DFc map.
My question is
1)
On 29/05/12 19:49, Dayana Nisbar wrote:
I need help with finding water in my protein structure using Coot.
I tried to find water with peaks above 1.6 sigma for both the 2Fo-Fc and
mFo-DFc maps.
The result were 253 water molecules found for 2Fo-Fc map and 563 water
molecules found for mFo-DFc
Hello,
My Akta Purifier is being repaired, and I'm thinking about borrowing a
colleague's HPLC in the interim. What makes the Aktas different from HPLCs?
I've used HPLCs for purifying small molecules and peptides but not
proteins. Anything I should be careful about regarding keeping the
machi
Hi, Ho,
Your question has a lot of variables.
"HPLC" columns should not be used on the Akta within my field of view
because the Akta within my field of view does not have gradual pump
acceleration and deceleration. "HPLC" columns can be damaged by sudden
changes in pressure or composition.
What makes the Aktas different from HPLCs?
Nothing. Akta Purifyer *is* HPLC.
Dima
Back in Iowa State University we used Waters HPLC for protein purification
during many years without noticeable damage to the stainless steel tubings. But
Dan was right about the pumps, someone in the lab forgot to flush the high salt
pump with water after its use and damaged the pump...
Alex
Thank you all for your input.
On Wednesday, May 30, 2012, Paul Emsley wrote:
> On 29/05/12 19:49, Dayana Nisbar wrote:
>>
>> I need help with finding water in my protein structure using Coot.
>>
>> I tried to find water with peaks above 1.6 sigma for both the 2Fo-Fc and
mFo-DFc maps.
>>
>> The r
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,
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
Thank you very much for your reply.
In my own understanding,
We collect the peak dataset, because of the large F'', and we can get
strong anomalous signal.
We collect the edge dataset, because of the large F', and combined with the
remote dataset, we can use the method just like SIR to get some
Hi,
you are right, the peak dataset corresponds to the highest f'' value.
However, this does not mean that f'' is null for the other
wavelengthes... you still have significant anomalous signal at the edge
and for the high energy remote wavelength... this will help your
phasing, so use it !
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
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?
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
Very neat.
Is there some way to set parameters not listed under 'Settings'? Data from
the Australian Synchrotron uses ROTATION_AXIS=-1.0 0.0 0.0 but I haven't
figured out how to change this. Editing the generated XDS.INP between runs
doesn't seem to do it.
Cheers,
/Daniel
--
Daniel Ericsson
Pos
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