WELL - with such high LLG and translation NCSthe high R factors are a bit
surprising..
The Patterson info does not give the relative height of the origin peak to
the off origin one..
Questions which I would check.
Look at the data processing carefully. Are there bad batches? Could the
space group
Hi Bashir,
It does look like you have translational pseudo-symmetry. If the translation
vector happens to be body-centering, it could affect your intensity statistics
so that the R-values would never go down as half of your reflections follow the
distribution for centric reflections. I had
Dear Eleanor,
Many thanks for you comments.
I have run aimless/pointless with those data sets having unit cell (134/67,
134/67, 183, 90, 90 120) previously integrated with P31 2 1.
Previously, I forced aimless to not determine laue group, to keep the original
SG, and now I let aimless
Donghyuk - testing your "twinning" in a lower symmetry space group can be
misleading.
Many checks look to see if twin related reflections are similar.
But the twin laws are often the same as the symmetry operators, so if you
have ignored the true symmetry, you will wrongly assume you have
Dear Randy,
Thank you for the important information and the useful link. I have another
question to bother you.
How accurately can these twining assessment programs report the data? What
could prevent these programs from reporting twinning data? (Twinned data are
reported as untwinned data)
Dear Lan,
Yes, that’s a serious problem that has led some people astray, including a few
papers where people got apparently good R-factors by invoking non-existent
twinning.
You can find a brief discussion of this point on the CCP4 wiki
Hi Randy,
> As Jacob and others have mentioned, you will always get lower R-factors once
> you treat the data as being twinned, and the more twin operators the bigger
> the reduction in R-factors.
Do normal data with no twinning, but refined with twin operator(s), show
similar phenomenon?
Donghyuk:
How good were your original images? If the paeks are sharp and clean, your processing could be easier; or you need more efforts. The data processing statistics is more important for troubleshooting.
Your showed an apparent SG of p6322, but it does have to be exact, especially when
quot; (N)CS.
> >
> > Hope this makes my remark a little clearer.
> >
> > Best,
> > Herman
> >
> > PS: While other BB readers may have had the same question, I have posted
> > the reply to the BB. I hope you don't mind.
> >
> >
> > -U
[mailto:p.du...@ibmc-cnrs.unistra.fr]
Gesendet: Freitag, 11. Januar 2019 11:52
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS &
twinning
Le Vendredi 11 Janvier 2019 09:07 CET, herman.schreu...@sanofi.com a écrit:
That P6322 Xtriage shows pretty clearly that you have good data, and that
it is not twinned..
So I think you stick with that spacegroup - introducing false twin laws to
explain true crystal symmetry reduces the R values at the expense of
getting clear electron density.
You could process the
Hi,
I'm just catching up on the BB after the CCP4 Study Weekend!
Going back to the beginning of this thread, it's true that tNCS and twinning
have opposite effects on the intensity moments, which can mask each other.
However, for simple cases (as this one appears to be) with a single NCS
st,
> Herman
>
> PS: While other BB readers may have had the same question, I have posted the
> reply to the BB. I hope you don't mind.
>
>
> -Ursprüngliche Nachricht-
> Von: Guan, Lan [mailto:lan.g...@ttuhsc.edu]
> Gesendet: Donnerstag, 10. Januar 2019 20:53
> An: Sc
ar 2019 20:53
An: Schreuder, Herman /DE
Betreff: Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning
Dear Herman,
I have read your insightful comments on twining and tNCS for years now, which
is very useful and helpful! Thanks,
For Donghyuk’s case, do you think that he really
Dear all,
Thank you very much for all of your suggestions and sharing experiences.
As many of you commented, the current small unit cell C2 refinement seems to be
incorrect or correct, and I should put some efforts to crack this question.
- To Phill Jeffrey,
The idea, trying to find high
For two projects in the distant past, we dealt with tNCS by initially telling
lies to the software (1szp and 3pkz). The tNCS was strong enough that there
was a clear weak/dark pattern in the diffraction pattern, so for the initial
molecular replacement we used a data set in the smaller unit
On Thursday, January 10, 2019 2:11:52 AM PST Donghyuk Shin wrote:
> Dear all,
>
> I am having tough time with my Xtal data sets those seem to be twinned or
> have translational NCS, and it will be greatly appreciated if you can give me
> some advices or comments!
>
> Data was initially
Donghyuk
The combination of two things gives me cause for concern:
1. You've reindexed something that apparently scaled OK in point group
622 into point group 2, with a smaller cell. Since it's hard to fake
that sort of data agreement in 622, I assume your data is at the very
least
lly.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Donghyuk
Shin
Gesendet: Donnerstag, 10. Januar 2019 11:12
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] translational NCS & twinning
Dear all,
I am having toug
Dear Jacob Keller and Vipul,
Thank you both very much for the reply.
Regarding the R-values, I am just wondering whether the huge gap between
refinements w/ w/o twin operator can be possible even the crystal is not
twinned?
Best wishes,
Donghyuk
>>I feel you went ahead with right strategy.
I agree with this part regarding lowering symmetry.
>>For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong
>>indicator, i believe.
This is not true—even non-twinned data will improve in R values with twinning
operators added as
Hi Donghyuk,
I feel you went ahead with right strategy.
For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong
indicator, i believe.
If you have already build all possible model, using tls can be of further
help.
Cheers,
Vipul
On Thu 10 Jan, 2019, 3:52 PM Donghyuk Shin Dear all,
Im Auftrag von Mark
Wilson
Gesendet: Donnerstag, 3. September 2015 19:56
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] Translational NCS with one molecule in ASU
Dear Remy,
Indeed, I think you may be correct and we're pursuing this now. A perfect
0.5 lattice translocation along b
10:06
An: CCP4BB@JISCMAIL.AC.UK
Betreff: AW: [ccp4bb] AW: [ccp4bb] Translational NCS with one molecule in ASU
Dear Mark and Remy,
This is what I meant by statistical disorder. It goes back to a rather cryptic
remark by Zbyszek Otwinowski (Jacob, you should have googled Otwinowski instead
of Ajees
board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
>Mark Wilson
>Gesendet: Donnerstag, 3. September 2015 02:06
>An: CCP4BB@JISCMAIL.AC.UK
>Betreff: Re: [ccp4bb] Translational NCS with one molecule in ASU
>
>Dear CCP4 Community,
>I've had a number of helpful responses (on- and off-
Hi All,
An important point is that the cell dimensions are: 54.98 58.45 66.89 90
90 90. While a and b are similar, they are (in my opinion) not similar
enough to support pseudo-merohedral twinning. The absences are indeed
absent, with I/sigma(I) between ~ -1 and 2. All three axes have similarly
t;> same
>>>> protein, space group and cell dimensions, and calculate pattersons
>>>>with
>>>> those. Sometimes strong peaks appear in pattersons for no obvious
>>>> reasons.
>>>> I would also consider statistical disorder, which will not show up in
r Mark,
>>>>>
>>>>> In this case you will have to apply Baysian statistics: given the
>>>>> prior:
>>>>> same protein, same space group same cell dimensions and molecular
>>>>> replacement fails completely, the likelihood of having
t;>>
>>>>>> Mark A. Wilson
>>>>>> Associate Professor
>>>>>> Department of Biochemistry/Redox Biology Center
>>>>>> University of Nebraska
>>>>>> N118 Beadle Center
>>>>>> 1901 Vine Stre
:08 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] AW: [ccp4bb] Translational NCS and molecular
replacement.
Dear Sudipta,
you are correct, your original scala.mtz has the wrong space group in it,
resulting in very high Rfactors (and presumably bad electron density).
In these cases
:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *
herman.schreu...@sanofi.com
*Sent:* Wednesday, July 16, 2014 3:08 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] AW: [ccp4bb] Translational NCS and molecular
replacement.
Dear Sudipta,
you are correct, your original
packing.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sudipta
Bhattacharyya
Gesendet: Dienstag, 15. Juli 2014 20:32
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Translational NCS and molecular replacement.
Dear Community,
I have some doubts to clarify. In a way
board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com
Sent: Wednesday, July 16, 2014 3:08 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] Translational NCS and molecular replacement.
Dear Sudipta,
you are correct, your original scala.mtz has the wrong space group
Dear Community,
I have some doubts to clarify. In a way to solve a structure by Phaser-MR,
I found phaser ended up with a potentially good MR solution (with good
statistics, packing and electron density, and as we know the homolog
structure so in a reasonable biological assembly also). However,
pdbset xyzin mol1.pdb xyzout mol1-tran1.pdb
SHIFT frac x,y,z (where x,y,z is the patterson peak)
end
OR
pdbset xyzin mol1.pdb xyzout mol1-tran2.pdb
SHIFT frac -x,-y,-z (since -x,-y,-z is also a the patterson peak)
end
Nicolas Soler wrote:
Dear CCP4bbs,
I am dealing with a case involving
Dear CCP4bbs,
I am dealing with a case involving pseudo-translational symmetry.
I wanted to know what was the simplest way to draw NCS copies of a
molecule deduced from the positions I observed in native Patterson. Is
there a translate option where on can give fractional coordinates in
Coot
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