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))
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
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,
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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
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
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
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
Thanks for your help.
How to use CAD to invert the hand?
2012/5/29 Ian Tickle ianj...@gmail.com
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
Thanks for your help.
How to override the warning?
2012/5/29 Mark J van Raaij mjvanra...@cnb.csic.es
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
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
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 p...@mrc-lmb.cam.ac.uk 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
P3 is another possible alternate indexing? is that correct?
2012/5/29 Ian Tickle 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
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 caiq...@gmail.com wrote:
P3 is another possible alternate indexing? is that correct?
2012/5/29 Ian Tickle ianj...@gmail.com
On 29 May 2012, at 15:02, Ian Tickle wrote:
Phil,
On 29 May 2012 14:08, Phil Evans p...@mrc-lmb.cam.ac.uk 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
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
Phil,
On 29 May 2012 15:09, Phil Evans p...@mrc-lmb.cam.ac.uk 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_
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 is
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
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
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
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
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
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
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
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.
The
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
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
How do you know the point group is 321?
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