Re: [ccp4bb] twinning or not?

[Nichols, Charlie]

Hi Len,

Twinning does not have to be a random spatial distribution within a crystal. 
You can have large discrete domains that are effectively untwinned smaller 
crystals assembled into the larger one – we have had several cases with 
back-to-back growth of two crystals. In some cases, the boundaries between such 
macro-twin domains can have weaker crystal contacts than within each domain 
allowing ‘physical-detwinning’ by application of stress:
https://pubmed.ncbi.nlm.nih.gov/15339801/

We have also had some success with breaking large, twinned crystals with a loop 
and collecting data from several individual chunks to obtain an untwinned 
dataset.

Synchrotron beam is much smaller than in-house so in your case you were 
presumably lucky with the orientation / choice of centring, so you collected 
data mostly from one such macro-twin domain.

Cheers, Charlie.

From: CCP4 bulletin board  On Behalf Of Thomas, Leonard 
M.
Sent: Monday, March 25, 2024 7:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] twinning or not?

WARNING: This message was sent by an external party. Report suspicious messages 
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Hello,

I have run into a very odd situation.  Upon collection and data processing on a 
crystal on my home source all pointers seemed to show twinning.  Was not 
surprised since previous crystals under different but related conditions have 
showed significant twinning though the cell dimensions were different but not 
the resulting apparent space group.

Now the odd thing, I sent the crystal to the synchrotron figuring I might be 
able to get some data that might help figure out what is going on.  Upon 
processing of the synchrotron data, SSRL 9-2, magically no twining was 
detected.  A couple of other crystals of the same compound though not from the 
same exact condition showed the twinning.  I processed the data using HKL, 
which I primarily on my home source data and XDS with similar results.

In summary, the exact same crystal shows twinning on Cu home source and no 
twinning at all at the synchrotron.

Any ideas would be welcomed.

Len

Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl



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Re: [ccp4bb] twinning or not?

[Phil Evans]

You can get apparent twinning if neighbouring spots are overlapped in any direction, and that may be worse with a home source with larger beam divergence. In that case a weak reflection may be corrupted by a neighbouring strong reflection, leading to intensity statistics characteristic of twinningPhilSent from my iPadOn 25 Mar 2024, at 19:24, Thomas, Leonard M.  wrote:CAUTION: This email originated from outside of the LMB:
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Do not click links or open attachments unless you recognize the sender and know the content is safe.If you think this is a phishing email, please forward it to phish...@mrc-lmb.cam.ac.uk
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Hello,


I have run into a very odd situation.  Upon collection and data processing on a crystal on my home source all pointers seemed to show twinning.  Was not surprised since previous crystals under different but related conditions have showed significant
 twinning though the cell dimensions were different but not the resulting apparent space group.  


Now the odd thing, I sent the crystal to the synchrotron figuring I might be able to get some data that might help figure out what is going on.  Upon processing of the synchrotron data, SSRL 9-2, magically no twining was detected.  A couple of
 other crystals of the same compound though not from the same exact condition showed the twinning.  I processed the data using HKL, which I primarily on my home source data and XDS with similar results.  


In summary, the exact same crystal shows twinning on Cu home source and no twinning at all at the synchrotron.


Any ideas would be welcomed.


Len






Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price
 Family Foundation Institute of Structural Biology
University
 of Oklahoma
Department
 of Chemistry and Biochemistry
101
 Stephenson Parkway
Norman,
 OK 73019-5251
Office:
 (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl









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Re: [ccp4bb] twinning or not?

[Kay Diederichs]

Hi Len,

a possible theory: your crystals may be macroscopically twinned, i.e. 
consisting of single crystals attached to each other in the way that the twin 
operation describes.
At your home source, you employ a rather big beam that hits more than one 
single crystal. So the data appear twinned. At the synchrotron however, the 
beam is way smaller, and may hit only a single crystal. Hence, untwinned data.

HTH, Kay

On Mon, 25 Mar 2024 19:22:54 +, Thomas, Leonard M.  wrote:

>Hello,
>
>I have run into a very odd situation.  Upon collection and data processing on 
>a crystal on my home source all pointers seemed to show twinning.  Was not 
>surprised since previous crystals under different but related conditions have 
>showed significant twinning though the cell dimensions were different but not 
>the resulting apparent space group.
>
>Now the odd thing, I sent the crystal to the synchrotron figuring I might be 
>able to get some data that might help figure out what is going on.  Upon 
>processing of the synchrotron data, SSRL 9-2, magically no twining was 
>detected.  A couple of other crystals of the same compound though not from the 
>same exact condition showed the twinning.  I processed the data using HKL, 
>which I primarily on my home source data and XDS with similar results.
>
>In summary, the exact same crystal shows twinning on Cu home source and no 
>twinning at all at the synchrotron.
>
>Any ideas would be welcomed.
>
>Len
>
>Leonard Thomas, Ph.D.
>Biomolecular Structure Core, Director
>Oklahoma COBRE in Structural Biology
>Price Family Foundation Institute of Structural Biology
>University of Oklahoma
>Department of Chemistry and Biochemistry
>101 Stephenson Parkway
>Norman, OK 73019-5251
>Office: (405)325-1126
>lmtho...@ou.edu
>http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>https://www.jiscmail.ac.uk/policyandsecurity/
>



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Re: [ccp4bb] Twinning or not?

[Eleanor Dodson]

You are right ; extremely accurate NCS parallel to a symmetry axis does 
distort the plots, but its effect is usually resolution dependent so 
expected straight lines are often not straight..


And pseudo NCS translation can be even more confusing.

Andrei Lebedev has done a lot of analysis  on this - some published in 
the CCP4 study weekend 2006 I think. Some to be published soon I think.


But if there is only one molecule in the asymmetric unitr the NCS cannot 
be present.


 Eleanor

Ian Tickle wrote:

-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]


On
  

Behalf Of Eleanor Dodson
Sent: 23 April 2009 15:59
To: Kumar
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Twinning or not?

Look at the moment plots after scalepack2mtz; if these are normal it
seems very unlikely you have twinning..
 Eleanor



I know this subject has been beaten to death in previous BB discussions,
but is it always as clear-cut as this?  If for example you had a NCS
2-fold co-incident with the twinning axis wouldn't that bias the moment
stats?  The derivation of the moment stats in the twinned case assumes
that the pairs of twin-related intensities (assuming we're talking about
the hemihedral case) are statistically independent, but that assumption
is clearly invalidated if there's NCS parallel to the twinning axis, and
in that situation the moment stats would tend towards the untwinned case
(depending of course on the exactness of the NCS and the resolution).
It's of no consolation to someone to tell them that their situation is
very unlikely if it actually happens to them!

It seems reasonable to say that if the moment stats conform to the
twinned case, then twinning is almost certainly present (barring data
processing blunders); however if the moment stats conform to the
untwinned case then you can't say for sure that it's not twinned,
there's still a chance (maybe small) that it's twinned even if the data
has been correctly processed.

I've read on several occasions that twinning and NCS are quite likely to
occur together, but I wonder if anyone has done a proper analysis and in
particular looked at cases where the twinning & NCS axes coincide to see
the effect on the moment stats?

Cheers

-- Ian


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Re: [ccp4bb] Twinning or not?

[Ian Tickle]

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Eleanor Dodson
> Sent: 23 April 2009 15:59
> To: Kumar
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Twinning or not?
> 
> Look at the moment plots after scalepack2mtz; if these are normal it
> seems very unlikely you have twinning..
>  Eleanor

I know this subject has been beaten to death in previous BB discussions,
but is it always as clear-cut as this?  If for example you had a NCS
2-fold co-incident with the twinning axis wouldn't that bias the moment
stats?  The derivation of the moment stats in the twinned case assumes
that the pairs of twin-related intensities (assuming we're talking about
the hemihedral case) are statistically independent, but that assumption
is clearly invalidated if there's NCS parallel to the twinning axis, and
in that situation the moment stats would tend towards the untwinned case
(depending of course on the exactness of the NCS and the resolution).
It's of no consolation to someone to tell them that their situation is
very unlikely if it actually happens to them!

It seems reasonable to say that if the moment stats conform to the
twinned case, then twinning is almost certainly present (barring data
processing blunders); however if the moment stats conform to the
untwinned case then you can't say for sure that it's not twinned,
there's still a chance (maybe small) that it's twinned even if the data
has been correctly processed.

I've read on several occasions that twinning and NCS are quite likely to
occur together, but I wonder if anyone has done a proper analysis and in
particular looked at cases where the twinning & NCS axes coincide to see
the effect on the moment stats?

Cheers

-- Ian


Disclaimer
This communication is confidential and may contain privileged information 
intended solely for the named addressee(s). It may not be used or disclosed 
except for the purpose for which it has been sent. If you are not the intended 
recipient you must not review, use, disclose, copy, distribute or take any 
action in reliance upon it. If you have received this communication in error, 
please notify Astex Therapeutics Ltd by emailing 
i.tic...@astex-therapeutics.com and destroy all copies of the message and any 
attached documents. 
Astex Therapeutics Ltd monitors, controls and protects all its messaging 
traffic in compliance with its corporate email policy. The Company accepts no 
liability or responsibility for any onward transmission or use of emails and 
attachments having left the Astex Therapeutics domain.  Unless expressly 
stated, opinions in this message are those of the individual sender and not of 
Astex Therapeutics Ltd. The recipient should check this email and any 
attachments for the presence of computer viruses. Astex Therapeutics Ltd 
accepts no liability for damage caused by any virus transmitted by this email. 
E-mail is susceptible to data corruption, interception, unauthorized amendment, 
and tampering, Astex Therapeutics Ltd only send and receive e-mails on the 
basis that the Company is not liable for any such alteration or any 
consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
Cambridge CB4 0QA under number 3751674

Re: [ccp4bb] Twinning or not?

[Eleanor Dodson]

Look at the moment plots after scalepack2mtz; if these are normal it 
seems very unlikely you have twinning..

Eleanor


Kumar wrote:

Hi,

I am trying to solve a protein-RNA complex structure - space group is either
P4(1)22 or P4(3)22. Even though data seems to have enough Se-anomalous
signal, we are unable to get any solution. I have tried even lower symmetry
such as P4(1), P4(3), P4, P222(1), C222(1), and P2(1).
Now I am worried if my data is twinned. Cumulative intensity distribution
(using scalepack2mtz) looks normal in all the space groups. Data analysis
using phenix.xtriage indicates presence of perfect twinning or higher
symmetry when analyzed in space group P4(1) or P4(3). As I have read, when
twin axis is parallel to one of the symmetry axis, data can show
artificially higher symmetry and cumulative intensity distribution in such
cases shows normal profile. I can work on improving anomalous signal if it
is not good enough but before that I want to be sure if data is not twinned.
Now how do I make sure that my data is fine and not twinned.

I need your suggestions.

Thank you
Kuma
  

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