Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

I am asked to test ZANADU which is meant to sort out spacegroup anomalies!
Maybe your example can be the test case..
Eleanor

On Fri, 24 Mar 2023 at 14:21, Gianluca Cioci  wrote:

> Hi Eleanor, Hi All,
>
> As suggested by Andrew (thanks!), I've switched off the NCS in Phaser and
> this gave a solution in C2 (a=66.2 b=83.9  c=66.2   90  98.7  90) that
> refines much better than the others (R=0.32/0.39).
>
> Still, I am not 100% convinced this is the correct cell/spacegroup... but
> it's a good starting point to continue the investigation.
>
> Thanks to all for your help !
>
> GIA
>
>
>
>
> Le 22/03/2023 à 07:10, Eleanor Dodson a écrit :
>
> You have tried all spacegroups within point groups? P2 p21 c222 c2221?.
>
> On Wed, 22 Mar 2023 at 03:01, Lijun Liu  wrote:
>
>> If data processing to be ok and all possible monoclinic and orthorombic
>> SG gave unreasonable high Rs, maybe good to give a try with p1 space group?
>>  Since the p-lattice indexing gave same a and  b also very close alpha
>> and beta, it could not exclude the possibility of p1 then twinned (also
>> together with ncs and tNCS) to show higher symmetry?
>>
>> Sent from my iPhone
>>
>> On Mar 21, 2023, at 1:25 PM, Jessica Bruhn 
>> wrote:
>>
>> 
>>
>> Hi Gianluca,
>>
>> Have you checked for diffraction anisotropy problems? It might be worth
>> running it through the STARANISO webserver:
>> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy
>> can make your data look twinned and elliptical truncation can help improve
>> maps.
>>
>> Good luck!
>>
>> Best,
>> Jessica
>>
>> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Hello, can you give us a screenshot of a diffraction image, with the
>>> caveat that they never look all that good with fine-slicing, still it might
>>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>>> space groups.
>>>
>>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>>
>>> Sent from Proton Mail mobile
>>>
>>>
>>>
>>>  Original Message 
>>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
>>>
>>> Dear All,
>>>
>>> I have collected a dataset from a small protein diffracting at 2.7A
>>> resolution, here is the space-group determination from XDS:
>>>
>>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>>
>>> Clearly, something weird is going on...
>>>
>>> The structure can be solved in C2/P21/C2221 with different number of
>>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>>
>>> However the maps look bad and the structure is impossible to refine
>>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>>
>>> Thanks in advance for any advice on how to rescue these data !
>>>
>>> Cheers,
>>>
>>> GIA
>>>
>>>
>>> [image: Click to zoom the image]
>>>
>>>
>>> --
>>> Dr. Gianluca CIOCI
>>> Toulouse Biotechnology Institute 
>>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>>
>>> Tel: +33 (0)5 61 55 97 68
>>> E-mail: ci...@insa-toulouse.fr
>>>
>>> TBI - INSA Toulouse135 avenue de Rangueil 
>>> 
>>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>> --
>>>
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>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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>>>
>> --
>>
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> To unsubscribe from the CCP4BB list, click the following link:
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>
> --
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute 
> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>
> Tel: +33 

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Gianluca Cioci]

Hi Eleanor, Hi All,

As suggested by Andrew (thanks!), I've switched off the NCS in Phaser 
and this gave a solution in C2 (a=66.2 b=83.9  c=66.2   90 98.7  90) 
that refines much better than the others (R=0.32/0.39).


Still, I am not 100% convinced this is the correct cell/spacegroup... 
but it's a good starting point to continue the investigation.


Thanks to all for your help !

GIA




Le 22/03/2023 à 07:10, Eleanor Dodson a écrit :

You have tried all spacegroups within point groups? P2 p21 c222 c2221?.

On Wed, 22 Mar 2023 at 03:01, Lijun Liu  wrote:

If data processing to be ok and all possible monoclinic and
orthorombic SG gave unreasonable high Rs, maybe good to give a try
with p1 space group? Since the p-lattice indexing gave same a and
 b also very close alpha and beta, it could not exclude the
possibility of p1 then twinned (also together with ncs and tNCS)
to show higher symmetry?

Sent from my iPhone


On Mar 21, 2023, at 1:25 PM, Jessica Bruhn
 wrote:


Hi Gianluca,

Have you checked for diffraction anisotropy problems? It might be
worth running it through the STARANISO webserver:
https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi.
Anisotropy can make your data look twinned and elliptical
truncation can help improve maps.

Good luck!

Best,
Jessica

On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

Hello, can you give us a screenshot of a diffraction image,
with the caveat that they never look all that good with
fine-slicing, still it might help ;-0 Also, an idea of the
R-merge, R-meas, CC-half in some of those space groups.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile



 Original Message 
On 21 Mar 2023, 16:43, Gianluca Cioci <
8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:


Dear All,

I have collected a dataset from a small protein
diffracting at 2.7A resolution, here is the space-group
determination from XDS:

 *  44    aP  0.0  66.3 66.3   83.9 
90.2  90.1  98.7
 *  31    aP  1.2  66.3 66.3   83.9 
89.8  90.1  81.3
 *  14    mC 1.3  86.4 100.6   83.9 
90.0  90.2  90.0
 *  34    mP 2.9  66.3 83.9   66.3  90.2 
98.7  90.1
 *  13    oC  3.7  86.4 100.6   83.9 
90.0  90.2  90.0
 *  10    mC 4.9 100.6 86.4   83.9  89.8 
90.0  90.0

Clearly, something weird is going on...

The structure can be solved in C2/P21/C2221 with
different number of molecules in the AU, with Phaser
complaining about strong tNCS modulation.

However the maps look bad and the structure is impossible
to refine (Rfact > 0.5) in all the space-groups that I
have tried so far...

Thanks in advance for any advice on how to rescue these
data !

Cheers,

GIA


Click to zoom the image


--
Dr. Gianluca CIOCI
Toulouse Biotechnology Institute (TBI)

http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
PICT - Plateforme Intégrée de Criblage de Toulouse
http://www.pict.ipbs.fr/

Tel: +33 (0)5 61 55 97 68
E-mail:ci...@insa-toulouse.fr

TBI - INSA Toulouse
135 avenue de Rangueil  

31077 Toulouse CEDEX 04
http://www.toulouse-biotechnology-institute.fr





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To 

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

You have tried all spacegroups within point groups? P2 p21 c222 c2221?.

On Wed, 22 Mar 2023 at 03:01, Lijun Liu  wrote:

> If data processing to be ok and all possible monoclinic and orthorombic SG
> gave unreasonable high Rs, maybe good to give a try with p1 space group?  
> Since
> the p-lattice indexing gave same a and  b also very close alpha and beta,
> it could not exclude the possibility of p1 then twinned (also together with
> ncs and tNCS) to show higher symmetry?
>
> Sent from my iPhone
>
> On Mar 21, 2023, at 1:25 PM, Jessica Bruhn 
> wrote:
>
> 
>
> Hi Gianluca,
>
> Have you checked for diffraction anisotropy problems? It might be worth
> running it through the STARANISO webserver:
> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can
> make your data look twinned and elliptical truncation can help improve
> maps.
>
> Good luck!
>
> Best,
> Jessica
>
> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, can you give us a screenshot of a diffraction image, with the
>> caveat that they never look all that good with fine-slicing, still it might
>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>> space groups.
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail mobile
>>
>>
>>
>>  Original Message 
>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Dear All,
>>
>> I have collected a dataset from a small protein diffracting at 2.7A
>> resolution, here is the space-group determination from XDS:
>>
>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>
>> Clearly, something weird is going on...
>>
>> The structure can be solved in C2/P21/C2221 with different number of
>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>
>> However the maps look bad and the structure is impossible to refine
>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>
>> Thanks in advance for any advice on how to rescue these data !
>>
>> Cheers,
>>
>> GIA
>>
>>
>> [image: Click to zoom the image]
>>
>>
>> --
>> Dr. Gianluca CIOCI
>> Toulouse Biotechnology Institute 
>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>
>> Tel: +33 (0)5 61 55 97 68
>> E-mail: ci...@insa-toulouse.fr
>>
>> TBI - INSA Toulouse135 avenue de Rangueil 
>> 
>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> --
>>
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>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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>>
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>
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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Lijun Liu]

If data processing to be ok and all possible monoclinic and orthorombic SG gave unreasonable high Rs, maybe good to give a try with p1 space group?  Since the p-lattice indexing gave same a and  b also very close alpha and beta, it could not exclude the possibility of p1 then twinned (also together with ncs and tNCS) to show higher symmetry? Sent from my iPhoneOn Mar 21, 2023, at 1:25 PM, Jessica Bruhn  wrote:Hi Gianluca,Have you checked for diffraction anisotropy problems? It might be worth running it through the STARANISO webserver: https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can make your data look twinned and elliptical truncation can help improve maps. Good luck!Best,JessicaOn Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:Hello, can you give us a screenshot of a diffraction image, with the caveat that they never look all that good with fine-slicing, still it might help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those space groups. Best wishes, Jon Cooper. jon.b.coo...@protonmail.comSent from Proton Mail mobile Original Message On 21 Mar 2023, 16:43, Gianluca Cioci < 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
  

  
  
Dear All,
I have collected a dataset from a small protein diffracting at
  2.7A resolution, here is the space-group determination from XDS: 

 *  44    aP  0.0  66.3   66.3   83.9  90.2 
  90.1  98.7
   *  31    aP  1.2  66.3   66.3   83.9  89.8  90.1 
  81.3
   *  14    mC 1.3  86.4  100.6   83.9  90.0  90.2 
  90.0 
   *  34    mP 2.9  66.3   83.9   66.3  90.2  98.7 
  90.1
   *  13    oC  3.7  86.4  100.6   83.9  90.0  90.2 
  90.0
   *  10    mC 4.9 100.6   86.4   83.9  89.8  90.0 
  90.0
Clearly, something weird is going on... 

The structure can be solved in C2/P21/C2221 with different number
  of molecules in the AU, with Phaser complaining about strong tNCS
  modulation.
However the maps look bad and the structure is impossible to
  refine (Rfact > 0.5) in all the space-groups that I have tried
  so far... 

Thanks in advance for any advice on how to rescue these data !

Cheers,

GIA





--
Dr. Gianluca CIOCI
Toulouse Biotechnology Institute (TBI)
http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
PICT - Plateforme Intégrée de Criblage de Toulouse
http://www.pict.ipbs.fr/

Tel: +33 (0)5 61 55 97 68
E-mail: ci...@insa-toulouse.fr

TBI - INSA Toulouse
135 avenue de Rangueil
31077 Toulouse CEDEX 04
http://www.toulouse-biotechnology-institute.fr
  



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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

cell   66.3   66.3   83.9  90.2  90.1  98.7.  P2 or P21 cell
Cell volume:364551.812

 Data line--- cell 86.4  100.6   83.9  90.0  90.2  90.0. Cell volume double
- C2 or C222 or C2221 cell
Cell volume:729240.938. ie

How many residues in your model?
It is hard to decide much without seeing the data..
Eleanor


On Tue, 21 Mar 2023 at 18:25, Jessica Bruhn  wrote:

> Hi Gianluca,
>
> Have you checked for diffraction anisotropy problems? It might be worth
> running it through the STARANISO webserver:
> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can
> make your data look twinned and elliptical truncation can help improve
> maps.
>
> Good luck!
>
> Best,
> Jessica
>
> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, can you give us a screenshot of a diffraction image, with the
>> caveat that they never look all that good with fine-slicing, still it might
>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>> space groups.
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail mobile
>>
>>
>>
>>  Original Message 
>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Dear All,
>>
>> I have collected a dataset from a small protein diffracting at 2.7A
>> resolution, here is the space-group determination from XDS:
>>
>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>
>> Clearly, something weird is going on...
>>
>> The structure can be solved in C2/P21/C2221 with different number of
>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>
>> However the maps look bad and the structure is impossible to refine
>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>
>> Thanks in advance for any advice on how to rescue these data !
>>
>> Cheers,
>>
>> GIA
>>
>>
>> [image: Click to zoom the image]
>>
>>
>> --
>> Dr. Gianluca CIOCI
>> Toulouse Biotechnology Institute 
>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>
>> Tel: +33 (0)5 61 55 97 68
>> E-mail: ci...@insa-toulouse.fr
>>
>> TBI - INSA Toulouse
>> 135 avenue de Rangueil
>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Jessica Bruhn]

Hi Gianluca,

Have you checked for diffraction anisotropy problems? It might be worth
running it through the STARANISO webserver:
https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can
make your data look twinned and elliptical truncation can help improve
maps.

Good luck!

Best,
Jessica

On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, can you give us a screenshot of a diffraction image, with the
> caveat that they never look all that good with fine-slicing, still it might
> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
> space groups.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 21 Mar 2023, 16:43, Gianluca Cioci <
> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Dear All,
>
> I have collected a dataset from a small protein diffracting at 2.7A
> resolution, here is the space-group determination from XDS:
>
>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>
> Clearly, something weird is going on...
>
> The structure can be solved in C2/P21/C2221 with different number of
> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>
> However the maps look bad and the structure is impossible to refine (Rfact
> > 0.5) in all the space-groups that I have tried so far...
>
> Thanks in advance for any advice on how to rescue these data !
>
> Cheers,
>
> GIA
>
>
> [image: Click to zoom the image]
>
>
> --
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute 
> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>
> Tel: +33 (0)5 61 55 97 68
> E-mail: ci...@insa-toulouse.fr
>
> TBI - INSA Toulouse
> 135 avenue de Rangueil
> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>
>
> --
>
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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Jon Cooper]

Hello, can you give us a screenshot of a diffraction image, with the caveat 
that they never look all that good with fine-slicing, still it might help ;-0 
Also, an idea of the R-merge, R-meas, CC-half in some of those space groups.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 21 Mar 2023, 16:43, Gianluca Cioci wrote:

> Dear All,
>
> I have collected a dataset from a small protein diffracting at 2.7A 
> resolution, here is the space-group determination from XDS:
>
> * 44 aP 0.0 66.3 66.3 83.9 90.2 90.1 98.7
> * 31 aP 1.2 66.3 66.3 83.9 89.8 90.1 81.3
> * 14 mC 1.3 86.4 100.6 83.9 90.0 90.2 90.0
> * 34 mP 2.9 66.3 83.9 66.3 90.2 98.7 90.1
> * 13 oC 3.7 86.4 100.6 83.9 90.0 90.2 90.0
> * 10 mC 4.9 100.6 86.4 83.9 89.8 90.0 90.0
>
> Clearly, something weird is going on...
>
> The structure can be solved in C2/P21/C2221 with different number of 
> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>
> However the maps look bad and the structure is impossible to refine (Rfact > 
> 0.5) in all the space-groups that I have tried so far...
>
> Thanks in advance for any advice on how to rescue these data !
>
> Cheers,
>
> GIA
>
> [Click to zoom the image]
>
> --
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute (TBI)
> http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulouse
> http://www.pict.ipbs.fr/
> Tel: +33 (0)5 61 55 97 68
> E-mail:
> ci...@insa-toulouse.fr
> TBI - INSA Toulouse
> 135 avenue de Rangueil
> 31077 Toulouse CEDEX 04
> http://www.toulouse-biotechnology-institute.fr
>
> ---
>
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Re: [ccp4bb] TWIN?

[benjamin bax]

Hi, 
  I have had twinning with P61, which makes it look like P6122. This is with 
slightly asymmetric dimer. 
You could try mol replacement in P65, and refine with twinning on. Maps should 
look better if correct. Ben 

Sent from my iPhone

> On 9 Jun 2021, at 10:13, Randy John Read  wrote:
> 
> I agree with Kay that, with a good model, solving in P1 is likely to be the 
> easiest comprehensive solution.  If that doesn’t work, Phaser starts every 
> MR_AUTO job by making a list of all the subgroups, including the different 
> potential indexings (represented by Hall symbols), so you could also work 
> through those systematically.  You provide a “SPACEGROUP HALL” command with 
> one of the Hall symbols for each possibility, and Phaser will expand the data 
> from the higher symmetry and reindex as required.
> 
> Best wishes,
> 
> Randy Read
> 
>> On 9 Jun 2021, at 09:37, Kay Diederichs  
>> wrote:
>> 
>> Hi Almudena,
>> 
>> if it is a packing problem, you need to find the correct subgroup of P6522 
>> (179).
>> Take a look at 
>> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
>>  .
>> Subgroups of 179 are 20, 153, 154, 170, and recursively each of these has 
>> subgroups:
>> 20 has  4 and 5 as subgroups, 153 and 154 both have 5 and 145 as subgroups, 
>> 170 has  4 and 145 as subgroups - taken together, 4, 5 and 145.
>> These have 1 as subgroup.
>> So the true space group could be P1, P21, C2, P32, C2221, P3212, P3221, P65.
>> You could run molecular replacement with all of these. Unfortunately, there 
>> may be several ways to index the data in some of these space groups, and 
>> they may not be equivalent. For example, I think there are 3 non-equivalent 
>> ways to index in C2 or P21 if the Laue class is 6/m .
>> 
>> If there is twinning, the intensity statistics should tell about that - but 
>> they may be set off by tNCS. 
>> 
>> One way to overcome the mess of possible space groups and settings plus the 
>> twinning possibility is to index and solve the structure in P1. That should 
>> allow a packing without clashes, and one could identify the correct space 
>> group by running POINTLESS on the Fcalc, and/or Zanuda. Since you have a 
>> good model, I'd try that.
>> 
>> Hope this helps,
>> Kay
>> 
>>> On Tue, 8 Jun 2021 17:14:30 +0200, Almudena Ponce Salvatierra 
>>>  wrote:
>>> 
>>> Hello everyone,
>>> 
>>> I am working with an RNA-only structure, data are at 3 Angstroms, and at
>>> first, I thought was in the C2 space group (with 6 molecules in the AU).
>>> 
>>> I can't finish building! it, because the structure seems to get in the way
>>> of its neighbor symmetrically! See the attached picture, please! The only 4
>>> residues that the structure is missing "have to go there", where one
>>> structure meets the other one. The R factors for this spacegroup are around
>>> 0.3.
>>> 
>>> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
>>> in P622, do MR with Phaser (trying all possible space groups in that point
>>> group), and it finds a unique solution in space group P 65 2 2 with TFZ of
>>> 50 and LLG >3000. Of course, the problem persists (one molecule sort of
>>> interfering with the neighbor), not only that but also the refinement
>>> R-factors are substantially higher, 0.37.
>>> 
>>> I have to say that the refinement maps look better when I am working with
>>> the C2 spacegroup. I can't understand, though, what is happening at that
>>> "supposedly interface" between the two molecules. Has anybody experienced
>>> anything like this in the past? Can it be a twin? Is it something else?
>>> and... how to fix it?
>>> 
>>> Thank you very much in advance.
>>> 
>>> Best wishes,
>>> 
>>> Almudena
>>> 
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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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> 
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building   Fax: +44 1223 336827
> Hills Road   E-mail: 
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K. 

Re: [ccp4bb] TWIN?

[Randy John Read]

I agree with Kay that, with a good model, solving in P1 is likely to be the 
easiest comprehensive solution.  If that doesn’t work, Phaser starts every 
MR_AUTO job by making a list of all the subgroups, including the different 
potential indexings (represented by Hall symbols), so you could also work 
through those systematically.  You provide a “SPACEGROUP HALL” command with one 
of the Hall symbols for each possibility, and Phaser will expand the data from 
the higher symmetry and reindex as required.

Best wishes,

Randy Read

> On 9 Jun 2021, at 09:37, Kay Diederichs  
> wrote:
> 
> Hi Almudena,
> 
> if it is a packing problem, you need to find the correct subgroup of P6522 
> (179).
> Take a look at 
> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
>  .
> Subgroups of 179 are 20, 153, 154, 170, and recursively each of these has 
> subgroups:
> 20 has  4 and 5 as subgroups, 153 and 154 both have 5 and 145 as subgroups, 
> 170 has  4 and 145 as subgroups - taken together, 4, 5 and 145.
> These have 1 as subgroup.
> So the true space group could be P1, P21, C2, P32, C2221, P3212, P3221, P65.
> You could run molecular replacement with all of these. Unfortunately, there 
> may be several ways to index the data in some of these space groups, and they 
> may not be equivalent. For example, I think there are 3 non-equivalent ways 
> to index in C2 or P21 if the Laue class is 6/m .
> 
> If there is twinning, the intensity statistics should tell about that - but 
> they may be set off by tNCS. 
> 
> One way to overcome the mess of possible space groups and settings plus the 
> twinning possibility is to index and solve the structure in P1. That should 
> allow a packing without clashes, and one could identify the correct space 
> group by running POINTLESS on the Fcalc, and/or Zanuda. Since you have a good 
> model, I'd try that.
> 
> Hope this helps,
> Kay
> 
> On Tue, 8 Jun 2021 17:14:30 +0200, Almudena Ponce Salvatierra 
>  wrote:
> 
>> Hello everyone,
>> 
>> I am working with an RNA-only structure, data are at 3 Angstroms, and at
>> first, I thought was in the C2 space group (with 6 molecules in the AU).
>> 
>> I can't finish building! it, because the structure seems to get in the way
>> of its neighbor symmetrically! See the attached picture, please! The only 4
>> residues that the structure is missing "have to go there", where one
>> structure meets the other one. The R factors for this spacegroup are around
>> 0.3.
>> 
>> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
>> in P622, do MR with Phaser (trying all possible space groups in that point
>> group), and it finds a unique solution in space group P 65 2 2 with TFZ of
>> 50 and LLG >3000. Of course, the problem persists (one molecule sort of
>> interfering with the neighbor), not only that but also the refinement
>> R-factors are substantially higher, 0.37.
>> 
>> I have to say that the refinement maps look better when I am working with
>> the C2 spacegroup. I can't understand, though, what is happening at that
>> "supposedly interface" between the two molecules. Has anybody experienced
>> anything like this in the past? Can it be a twin? Is it something else?
>> and... how to fix it?
>> 
>> Thank you very much in advance.
>> 
>> Best wishes,
>> 
>> Almudena
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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 
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>> 
> 
> 
> 
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-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] TWIN?

[Kay Diederichs]

Hi Almudena,

if it is a packing problem, you need to find the correct subgroup of P6522 
(179).
Take a look at 
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
 .
Subgroups of 179 are 20, 153, 154, 170, and recursively each of these has 
subgroups:
20 has  4 and 5 as subgroups, 153 and 154 both have 5 and 145 as subgroups, 170 
has  4 and 145 as subgroups - taken together, 4, 5 and 145.
These have 1 as subgroup.
So the true space group could be P1, P21, C2, P32, C2221, P3212, P3221, P65.
You could run molecular replacement with all of these. Unfortunately, there may 
be several ways to index the data in some of these space groups, and they may 
not be equivalent. For example, I think there are 3 non-equivalent ways to 
index in C2 or P21 if the Laue class is 6/m .

If there is twinning, the intensity statistics should tell about that - but 
they may be set off by tNCS. 

One way to overcome the mess of possible space groups and settings plus the 
twinning possibility is to index and solve the structure in P1. That should 
allow a packing without clashes, and one could identify the correct space group 
by running POINTLESS on the Fcalc, and/or Zanuda. Since you have a good model, 
I'd try that.

Hope this helps,
Kay

On Tue, 8 Jun 2021 17:14:30 +0200, Almudena Ponce Salvatierra 
 wrote:

>Hello everyone,
>
>I am working with an RNA-only structure, data are at 3 Angstroms, and at
>first, I thought was in the C2 space group (with 6 molecules in the AU).
>
>I can't finish building! it, because the structure seems to get in the way
>of its neighbor symmetrically! See the attached picture, please! The only 4
>residues that the structure is missing "have to go there", where one
>structure meets the other one. The R factors for this spacegroup are around
>0.3.
>
>However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
>in P622, do MR with Phaser (trying all possible space groups in that point
>group), and it finds a unique solution in space group P 65 2 2 with TFZ of
>50 and LLG >3000. Of course, the problem persists (one molecule sort of
>interfering with the neighbor), not only that but also the refinement
>R-factors are substantially higher, 0.37.
>
>I have to say that the refinement maps look better when I am working with
>the C2 spacegroup. I can't understand, though, what is happening at that
>"supposedly interface" between the two molecules. Has anybody experienced
>anything like this in the past? Can it be a twin? Is it something else?
>and... how to fix it?
>
>Thank you very much in advance.
>
>Best wishes,
>
>Almudena
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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Re: [ccp4bb] TWIN?

[Eric Montemayor]

Maybe you have a bimolecular dimer when you expected a unimolecular
hairpin?  It’s happened before :)

https://pubmed.ncbi.nlm.nih.gov/31584014/

Eric



On Tue, Jun 8, 2021 at 10:15 AM Almudena Ponce Salvatierra <
maps.fa...@gmail.com> wrote:

> Hello everyone,
>
> I am working with an RNA-only structure, data are at 3 Angstroms, and at
> first, I thought was in the C2 space group (with 6 molecules in the AU).
>
> I can't finish building! it, because the structure seems to get in the way
> of its neighbor symmetrically! See the attached picture, please! The only 4
> residues that the structure is missing "have to go there", where one
> structure meets the other one. The R factors for this spacegroup are around
> 0.3.
>
> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
> in P622, do MR with Phaser (trying all possible space groups in that point
> group), and it finds a unique solution in space group P 65 2 2 with TFZ of
> 50 and LLG >3000. Of course, the problem persists (one molecule sort of
> interfering with the neighbor), not only that but also the refinement
> R-factors are substantially higher, 0.37.
>
> I have to say that the refinement maps look better when I am working with
> the C2 spacegroup. I can't understand, though, what is happening at that
> "supposedly interface" between the two molecules. Has anybody experienced
> anything like this in the past? Can it be a twin? Is it something else?
> and... how to fix it?
>
> Thank you very much in advance.
>
> Best wishes,
>
> Almudena
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] TWIN?

[Eleanor Dodson]

First spacegrouop -  trigonal spacegroups can also be indexed as C2 so it
isnt so surprising that a P6/mmm should masquerade as C2.
I would look very carefull at the POINTLESS symmetry scores and see if some
are more convincing than others.

But how I hate RNA & DNA - molecular replacement struggles because often
the molecules pack to form a pseudo-continuous chain so it is easy when
searching with one copy to finish up a residue or so out of register..
Do the B factors give you a clue about error?

And with only 3A data it will be hard to check the base identities.. Maybe
set base occupancies to 0.00 one at a time , refine then see what you see
in the difference map. Maybe you might detect a possible
different interpretation
Eleanor


On Tue, 8 Jun 2021 at 16:28, CRAIG A BINGMAN <
21371e2fba31-dmarc-requ...@jiscmail.ac.uk> wrote:

> It’s difficult to tell exactly what is happening from your description and
> the attached image. Both your description and the image are OK. It’s just
> that there are a lot of ways for things to go off the rails.
>
> Are the molecules stacked end-to-end? In that case, you may have an
> incommensurate structure where the molecule is disordered around a
> pseudo-continuous helical axis running through the crystal.
>
> But from this view, it looks like at least two bases are swung out to the
> left. I’d omit the interaction region, refine what you can model well as
> well as you can, and see if the maps for this region clear up. Keep in mind
> that your model might be out of register, so look at the shapes of the
> bases carefully to see if you need adjust that.
>
> On Jun 8, 2021, at 10:14 AM, maps.fa...@gmail.com wrote:
>
> Hello everyone,
>
> I am working with an RNA-only structure, data are at 3 Angstroms, and at
> first, I thought was in the C2 space group (with 6 molecules in the AU).
>
> I can't finish building! it, because the structure seems to get in the way
> of its neighbor symmetrically! See the attached picture, please! The only 4
> residues that the structure is missing "have to go there", where one
> structure meets the other one. The R factors for this spacegroup are around
> 0.3.
>
> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
> in P622, do MR with Phaser (trying all possible space groups in that point
> group), and it finds a unique solution in space group P 65 2 2 with TFZ of
> 50 and LLG >3000. Of course, the problem persists (one molecule sort of
> interfering with the neighbor), not only that but also the refinement
> R-factors are substantially higher, 0.37.
>
> I have to say that the refinement maps look better when I am working with
> the C2 spacegroup. I can't understand, though, what is happening at that
> "supposedly interface" between the two molecules. Has anybody experienced
> anything like this in the past? Can it be a twin? Is it something else?
> and... how to fix it?
>
> Thank you very much in advance.
>
> Best wishes,
>
> Almudena
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>  16.43.21.png>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] TWIN?

[CRAIG A BINGMAN]

It’s difficult to tell exactly what is happening from your description and the 
attached image. Both your description and the image are OK. It’s just that 
there are a lot of ways for things to go off the rails.

Are the molecules stacked end-to-end? In that case, you may have an 
incommensurate structure where the molecule is disordered around a 
pseudo-continuous helical axis running through the crystal.

But from this view, it looks like at least two bases are swung out to the left. 
I’d omit the interaction region, refine what you can model well as well as you 
can, and see if the maps for this region clear up. Keep in mind that your model 
might be out of register, so look at the shapes of the bases carefully to see 
if you need adjust that.

On Jun 8, 2021, at 10:14 AM, maps.fa...@gmail.com 
wrote:

Hello everyone,

I am working with an RNA-only structure, data are at 3 Angstroms, and at first, 
I thought was in the C2 space group (with 6 molecules in the AU).

I can't finish building! it, because the structure seems to get in the way of 
its neighbor symmetrically! See the attached picture, please! The only 4 
residues that the structure is missing "have to go there", where one structure 
meets the other one. The R factors for this spacegroup are around 0.3.

However, Phenix Xtriage suggests the symmetry may be higher. So I reindex in 
P622, do MR with Phaser (trying all possible space groups in that point group), 
and it finds a unique solution in space group P 65 2 2 with TFZ of 50 and LLG 
>3000. Of course, the problem persists (one molecule sort of interfering with 
the neighbor), not only that but also the refinement R-factors are 
substantially higher, 0.37.

I have to say that the refinement maps look better when I am working with the 
C2 spacegroup. I can't understand, though, what is happening at that 
"supposedly interface" between the two molecules. Has anybody experienced 
anything like this in the past? Can it be a twin? Is it something else? and... 
how to fix it?

Thank you very much in advance.

Best wishes,

Almudena



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Re: [ccp4bb] Twin law definition in REFMAC5

[Andrey Lebedev]

Dear Petr

Both questions, on twin law and R-factors, are mainly questions about 
definitions and standards.

From Online Dictionary of Crystallography: "The twin law is the SET of twin 
operations mapping two individuals of a twin." 

In your P 21 21 21 example with a=b, the set contains four operations:
2-fold rotations around [110] and [-110], and rotations around [001] by 90 and 
-90 degrees. These operations can be written as k,h,-l; -k,-h,-l; -k,h,l; 
k,-h,l. Four is because there are four operations in 222 point group. All four 
are equivalent twin operations for this particular twin. Any of them can be 
taken as a REPRESENTATIVE of the twin law, but it will be incorrect use of 
terminology to say that one of then IS a twin law.  It is valid to use any of 
them in calculations.

Again, the question about R-factors for data from twinned crystal is a question 
of definition. The standard definitions of R-cryst and R-free are NOT 
applicable to such data. (Let's leave alone the discussion on whether and when 
R-factors are useful statistics).

This is because the definitions of R-cryst and R-free use the notion of  
"observed" structure amplitudes. In case of non-twinned crystal, there is 
French-Wilson procedure (implemented in truncate program), which is a de-facto 
standard (good or bad - different story) for calculating "observed" structure 
amplitudes from "observed" intensities. To calculate the "observed" intensities 
from "twinned" intensities we need yet another standard, e.g. a standard 
de-twining procedure, which does not exist. Moreover, refinement programs do 
not use de-twinning, but, other way round, fit calculated "twinned" intensities 
to "observed" "twinned" intensities. This is robust. But when it goes to 
R-factors, there is range of options.

In Refmac, "twinned" refinement can be conducted against intensities or 
structure amplitudes, however calculated. The former is in theory more robust, 
but it uses definitions of R-factors that results in higher values, especially 
when there are many weak reflections.

For bureaucratic purposes, I may suggest the option of refinement against 
structure amplitudes (obtained e.g. using truncate). That will give lower 
R?factors. Alternatively, refinement against intensities can be followed by 
refmac job with zero cycles using structure amplitudes option.

Andrey

P.S. An important reminder from Garib: output mtz-file from refmac should not 
be used in subsequent refinements as input. It is only for map calculation and 
for internal use in model building pipelines. Please always use mtz-file form 
data reduction program (e.g. aimless) as input for refmac. This comment is 
especially relevant for "twin refinement".



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Re: [ccp4bb] Twin law definition in REFMAC5

[Petrus Zwart]

On Mon, Jul 6, 2020 at 10:33 PM Petr Kolenko 
wrote:

> Dear Eleanor,
> The unit cell parameters are 117.385  155.506  155.611  90.00  90.00
> 90.00, as you expected. The twin law was recognized using phenix.xtriage.
> If I refine the structure using phenix.refine with no twin law and the
> Rwork/free values were 28/33. With the twin law "-h,l,k" the R values are
> 22/28. Moreover, many weird features of the electron density map
> disappeared. But I used phenix.refine only as a proof, because I refined
> the structure using REFMAC5 from the beginning and I do not want to change
> the refinement program during the structure refinement.
>


you break my heart 

:-)




> Thank you for your response,
> Petr
>
> 
> From: Eleanor Dodson 
> Sent: Tuesday, July 7, 2020 7:08:44 AM
> To: Petr Kolenko
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Twin law definition in REFMAC5
>
> Is that twin law possible? Presumably the cell lengths for b and c are
> close but you are swapping a 2fold axis along c for a 21 axis along b?
> Eleanor
>
> On Tue, 7 Jul 2020 at 05:36, Petr Kolenko  <mailto:petr.kole...@fjfi.cvut.cz>> wrote:
> Dear colleagues,
> I have a crystal with space group P21212 and merohedral twinning according
> to "-h, l, k" twin law. If I click "twin" in the interface, REFMAC5
> recognizes a different twin law and does not refine the structure properly.
> Is there a way to tell REFMAC5 the proper twin law? I tried to find the
> information in the documentation, but I failed. This is an older project
> running under i, not i2.
> Best regards,
> Petr
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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> http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by
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-- 

P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246

PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
-



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Re: [ccp4bb] Twin law definition in REFMAC5

[Petr Kolenko]

Dear Eleanor,
The unit cell parameters are 117.385  155.506  155.611  90.00  90.00  90.00, as 
you expected. The twin law was recognized using phenix.xtriage. If I refine the 
structure using phenix.refine with no twin law and the Rwork/free values were 
28/33. With the twin law "-h,l,k" the R values are 22/28. Moreover, many weird 
features of the electron density map disappeared. But I used phenix.refine only 
as a proof, because I refined the structure using REFMAC5 from the beginning 
and I do not want to change the refinement program during the structure 
refinement.
Thank you for your response,
Petr


From: Eleanor Dodson 
Sent: Tuesday, July 7, 2020 7:08:44 AM
To: Petr Kolenko
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Twin law definition in REFMAC5

Is that twin law possible? Presumably the cell lengths for b and c are close 
but you are swapping a 2fold axis along c for a 21 axis along b? Eleanor

On Tue, 7 Jul 2020 at 05:36, Petr Kolenko 
mailto:petr.kole...@fjfi.cvut.cz>> wrote:
Dear colleagues,
I have a crystal with space group P21212 and merohedral twinning according to 
"-h, l, k" twin law. If I click "twin" in the interface, REFMAC5 recognizes a 
different twin law and does not refine the structure properly. Is there a way 
to tell REFMAC5 the proper twin law? I tried to find the information in the 
documentation, but I failed. This is an older project running under i, not i2.
Best regards,
Petr



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Re: [ccp4bb] Twin law definition in REFMAC5

[Eleanor Dodson]

Is that twin law possible? Presumably the cell lengths for b and c are
close but you are swapping a 2fold axis along c for a 21 axis along b?
Eleanor

On Tue, 7 Jul 2020 at 05:36, Petr Kolenko  wrote:

> Dear colleagues,
> I have a crystal with space group P21212 and merohedral twinning according
> to "-h, l, k" twin law. If I click "twin" in the interface, REFMAC5
> recognizes a different twin law and does not refine the structure properly.
> Is there a way to tell REFMAC5 the proper twin law? I tried to find the
> information in the documentation, but I failed. This is an older project
> running under i, not i2.
> Best regards,
> Petr
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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Re: [ccp4bb] Twin and tNCS

[Keller, Jacob]

I believe static/statistical disorder would produce good TFZs with poor packing.

See the paper below for example.

JPK

Sapan A Shah, Axel T Brunger, The 1.8 å crystal structure of a statically 
disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its 
effect on nucleic acid structure1, Journal of Molecular Biology, Volume 285, 
Issue 4, 29 January 1999, Pages 1577-1588, ISSN 0022-2836, 
http://dx.doi.org/10.1006/jmbi.1998.2385.
(http://www.sciencedirect.com/science/article/pii/S0022283698923853)
Abstract: The crystal structure of a 17 base RNA oligomer, r(CACCGGAUG 
GUUCGGUG), has been solved to a resolution of 1.8 Å through a combination of 
molecular replacement, multiple isomorphous replacement phasing, and analysis 
of observed intensity distributions. The oligomer, which forms a stem-loop in 
solution, crystallized as a pseudo-infinite duplex in spacegroup P321. The 
asymmetric unit of the crystal contains four superimposed orientations of the 
duplex that are out of register, such that backbones superimpose, but base 
identity differs. This static disorder was initially discovered by brominating 
a single residue per strand in the sequence, and observing four peaks per 
strand in difference maps phased with a native molecular replacement solution. 
The presence of four superimposed duplex “motifs” related by 
non-crystallographic hypersymmetry was detected by computing 〈I2〉/〈I〉2 and 
Wilson ratios for the observed intensities. The observed ratios matched those 
produced from calculated intensities of a 4-fold statically disordered model. 
Multi-conformer simulated annealing refinement against a maximum-likelihood 
target incorporating experimental phase information was used to refine the 
4-fold disordered model to an Rfree and R of 29.35% and 25.5%, respectively. 
The resulting structure reveals four distinct conformations of the duplex, with 
an average pairwise backbone rmsd of 2.35 Å. The structural differences between 
the four conformations, which can be attributed to differences in packing 
environment, highlight the possible influence of crystal packing forces on 
nucleic acid X-ray structures. Analysis of inter-helical packing between 
symmetry-related molecules reveals an RNA “zipper” that mediates direct 
phosphate oxygen-2′ hydroxyl interactions between close-packed phosphate-sugar 
backbones. This may be a general mode for RNA tertiary interaction that does 
not depend on metal ions or primary sequence.
Keywords: X-ray crystallography; RNA; disorder; intensity statistics; Wilson 
ratio





-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read
Sent: Thursday, April 21, 2016 3:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Twin and tNCS

Hi,

On your point 2, if this isn’t already a frequently asked question somewhere it 
should be!  With twinning, you have to decide first whether or not the crystal 
appears to be twinned.  This is done on the basis of the twin tests that depend 
only on the distribution of intensities but not on a twin law, such as the 
second moments test or the L-test.  If those tests say that your crystal is 
twinned, then you start to think about what the twin law is.

The tests based on twin laws compare the reflections related by twin laws to 
see if they are more closely related to each other than you would expect them 
to be randomly.  Unfortunately, if you have assigned a symmetry that is too 
low, then there are reflections that are unrelated by the symmetry you have 
assigned, but they are related by the symmetry that you have missed in your 
space group assignment, and those symmetry operators are also possible twin 
laws in the lower symmetry space group.  So the various tests that depend on 
twin laws will say that you have perfect twinning, because the supposedly 
“twin-related” reflections are almost perfectly correlated to each other.  If 
you reprocess your data in point group P622, you will find that there are no 
twin laws identified, and nothing in xtriage or truncate will say that your 
crystal is twinned.

As for the RMS value, I agree with Ray that the value of 1.5A often works well 
for NMR structures.  You could also try something more optimistic, like 1-1.25A.

I’m not sure why you’re getting solutions with high TFZ that fail to pack.  
However, I’d like to see the results of searching in what I think is the 
correct point group first.

Best wishes,

Randy

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 21 Apr 2016, at 17:49, Qixu Cai <caiq...@gmail.com> wrote:
> 
> Dear Dr. Read,
> 
> 1, Yes, I h

Re: [ccp4bb] twin or untwinned

[Yamei Yu]

Thanks all for your comments!



Yamei Yu


On Jul 5, 2014, at 5:10 AM, Nat Echols nathaniel.ech...@gmail.com wrote:

 On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols nathaniel.ech...@gmail.com wrote:
 On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de 
 wrote:
 yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL 
 intensities as amplitudes, producing very different output statistics, 
 compared both to the XDS statistics and to an mtz file with amplitudes 
 created from that XDS file.
 
 This is incorrect.  It does read it correctly as intensities - the confusion 
 probably arises from the fact that Xtriage internally converts everything to 
 amplitudes immediately, so that when it reports the summary of file 
 information, it will say xray.amplitude no matter what the input type was 
 (the same will also be true for Scalepack and MTZ formats).  However, the 
 data will be converted back to intensities as needed for the individual 
 analyses.  Obviously this isn't quite ideal either since the original 
 intensities are preferable but for the purpose of detecting twinning I hope 
 it will be okay.  In any case the incorrect feedback confused several other 
 users so it's gone as of a few weeks ago, and the current nightly builds will 
 report the true input data type.  (The actual results are unchanged.)
 
 Tim: I have no reason to think we handle unmerged data poorly; I'm not sure 
 who would have told you that.  In most cases they will be merged as needed 
 upon reading the file.  I'm a little concerned that you're getting such 
 different results from Xtriage and pointless/aimless, however.  Could you 
 please send me the input and log files off-list?  Dirk, same thing: if you 
 have an example where XDS and Xtriage are significantly in disagreement, the 
 inputs (and logs) would be very helpful.  In both cases, I suspect the 
 difference is in the use of resolution cutoffs and absolute-scaled 
 intensities in Xtriage versus other programs, but I'd like to be certain that 
 there's not something broken.
 
 I stand corrected: unmerged XDS files (but not other formats) were not being 
 handled appropriately in Xtriage; this was fixed several weeks ago, so the 
 nightly builds should behave as expected.
 
 -Nat 

Re: [ccp4bb] twin or untwinned

[Eleanor Dodson]

To answer the original question.
The indicators are that it is not twinned,
If the Mean s are close to the untwinned values - you can probably believe
it.

Why are you worried?
Eleanor

Determining possible twin laws.

  0 merohedral twin operators found
  0 pseudo-merohedral twin operators found
In total,   0 twin operator were found


 Mean |L|   :0.378  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.205  (untwinned: 0.333; perfect twin: 0.200)





On 3 July 2014 15:50, Nat Echols nathaniel.ech...@gmail.com wrote:

 On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de
 wrote:

 yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
 intensities as amplitudes, producing very different output statistics,
 compared both to the XDS statistics and to an mtz file with amplitudes
 created from that XDS file.


 This is incorrect.  It does read it correctly as intensities - the
 confusion probably arises from the fact that Xtriage internally converts
 everything to amplitudes immediately, so that when it reports the summary
 of file information, it will say xray.amplitude no matter what the input
 type was (the same will also be true for Scalepack and MTZ formats).
 However, the data will be converted back to intensities as needed for the
 individual analyses.  Obviously this isn't quite ideal either since the
 original intensities are preferable but for the purpose of detecting
 twinning I hope it will be okay.  In any case the incorrect feedback
 confused several other users so it's gone as of a few weeks ago, and the
 current nightly builds will report the true input data type.  (The actual
 results are unchanged.)

 Tim: I have no reason to think we handle unmerged data poorly; I'm not
 sure who would have told you that.  In most cases they will be merged as
 needed upon reading the file.  I'm a little concerned that you're getting
 such different results from Xtriage and pointless/aimless, however.  Could
 you please send me the input and log files off-list?  Dirk, same thing: if
 you have an example where XDS and Xtriage are significantly in
 disagreement, the inputs (and logs) would be very helpful.  In both cases,
 I suspect the difference is in the use of resolution cutoffs and
 absolute-scaled intensities in Xtriage versus other programs, but I'd like
 to be certain that there's not something broken.

 thanks,
 Nat

Re: [ccp4bb] twin or untwinned

[Eleanor Dodson]

Sorry - the stats DO indicate perfect twinning - I misread the first Email..

Please ignore that comment!
  Eleanor


On 4 July 2014 13:16, Philip Kiser p...@case.edu wrote:

 Hi Eleanor,

 If I'm not mistaken, the mean I stats​ are indicating perfect twinning.

 Philip


 On Fri, Jul 4, 2014 at 4:49 AM, Eleanor Dodson eleanor.dod...@york.ac.uk
 wrote:

 To answer the original question.
 The indicators are that it is not twinned,
 If the Mean s are close to the untwinned values - you can probably
 believe it.

 Why are you worried?
 Eleanor


 Determining possible twin laws.

   0 merohedral twin operators found
   0 pseudo-merohedral twin operators found
 In total,   0 twin operator were found


  Mean |L|   :0.378  (untwinned: 0.500; perfect twin: 0.375)
   Mean  L^2  :0.205  (untwinned: 0.333; perfect twin: 0.200)





 On 3 July 2014 15:50, Nat Echols nathaniel.ech...@gmail.com wrote:

 On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa 
 kostr...@genzentrum.lmu.de wrote:

 yes - unfortunately, in my hands, phenix.xtriage reads the
 XDS_ASCII.HKL intensities as amplitudes, producing very different output
 statistics, compared both to the XDS statistics and to an mtz file with
 amplitudes created from that XDS file.


 This is incorrect.  It does read it correctly as intensities - the
 confusion probably arises from the fact that Xtriage internally converts
 everything to amplitudes immediately, so that when it reports the summary
 of file information, it will say xray.amplitude no matter what the input
 type was (the same will also be true for Scalepack and MTZ formats).
 However, the data will be converted back to intensities as needed for the
 individual analyses.  Obviously this isn't quite ideal either since the
 original intensities are preferable but for the purpose of detecting
 twinning I hope it will be okay.  In any case the incorrect feedback
 confused several other users so it's gone as of a few weeks ago, and the
 current nightly builds will report the true input data type.  (The actual
 results are unchanged.)

 Tim: I have no reason to think we handle unmerged data poorly; I'm not
 sure who would have told you that.  In most cases they will be merged as
 needed upon reading the file.  I'm a little concerned that you're getting
 such different results from Xtriage and pointless/aimless, however.  Could
 you please send me the input and log files off-list?  Dirk, same thing: if
 you have an example where XDS and Xtriage are significantly in
 disagreement, the inputs (and logs) would be very helpful.  In both cases,
 I suspect the difference is in the use of resolution cutoffs and
 absolute-scaled intensities in Xtriage versus other programs, but I'd like
 to be certain that there's not something broken.

 thanks,
 Nat

Re: [ccp4bb] twin or untwinned

[Nat Echols]

On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols nathaniel.ech...@gmail.com
wrote:

 On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de
 wrote:

 yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
 intensities as amplitudes, producing very different output statistics,
 compared both to the XDS statistics and to an mtz file with amplitudes
 created from that XDS file.


 This is incorrect.  It does read it correctly as intensities - the
 confusion probably arises from the fact that Xtriage internally converts
 everything to amplitudes immediately, so that when it reports the summary
 of file information, it will say xray.amplitude no matter what the input
 type was (the same will also be true for Scalepack and MTZ formats).
 However, the data will be converted back to intensities as needed for the
 individual analyses.  Obviously this isn't quite ideal either since the
 original intensities are preferable but for the purpose of detecting
 twinning I hope it will be okay.  In any case the incorrect feedback
 confused several other users so it's gone as of a few weeks ago, and the
 current nightly builds will report the true input data type.  (The actual
 results are unchanged.)

 Tim: I have no reason to think we handle unmerged data poorly; I'm not
 sure who would have told you that.  In most cases they will be merged as
 needed upon reading the file.  I'm a little concerned that you're getting
 such different results from Xtriage and pointless/aimless, however.  Could
 you please send me the input and log files off-list?  Dirk, same thing: if
 you have an example where XDS and Xtriage are significantly in
 disagreement, the inputs (and logs) would be very helpful.  In both cases,
 I suspect the difference is in the use of resolution cutoffs and
 absolute-scaled intensities in Xtriage versus other programs, but I'd like
 to be certain that there's not something broken.


I stand corrected: unmerged XDS files (but not other formats) were not
being handled appropriately in Xtriage; this was fixed several weeks ago,
so the nightly builds should behave as expected.

-Nat

Re: [ccp4bb] twin or untwinned

[Philip Kiser]

Hi Yamei,

A possible explanation is that the actual space group is P4(2) but the data
are perfectly hemihedrally twinned, which makes the crystal appear to
possess 422 point group symmetry. No twin operators are found because
merohedral twinning is not possible in crystals with true 422 symmetry. If
you analyze the data after reprocessing in P4(2) a twin law will then be
found.

Philip


On Wed, Jul 2, 2014 at 11:04 PM, Yamei Yu ymyux...@gmail.com wrote:

 HI all,

I have a data set processed to P42 21 2 (the space group was suggested
 by pointless ). then I use phenix.xtriage to analysis the data. I was
 confused by the phenix.xtriage result.
 According to the following number it is twin data, but why it couldn’t
 find any possible twin law?

 Determining possible twin laws.

   0 merohedral twin operators found
   0 pseudo-merohedral twin operators found
 In total,   0 twin operator were found


  Mean |L|   :0.378  (untwinned: 0.500; perfect twin: 0.375)
   Mean  L^2  :0.205  (untwinned: 0.333; perfect twin: 0.200)


 How could be that? Is it twin or no twin?

 Please find the log file of phenix.xtrage in attachment.

 Thank you so much for your suggestion!


 

 Yamei Yu

Re: [ccp4bb] twin or untwinned

[Tim Gruene]

Hi Yamei,

did you by any chance feed the output file from XDS into xtriage? It
would indicate the data were twinned even for a near perfect insulin
test crystal. After discussion with the developers I understand that
phenix does not seem to handle unmerged data well.

With phenix.xtriage V. phenix-1.9-1692:, XDS_ASCII.HKL
  Mean |L|   :0.392  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.219  (untwinned: 0.333; perfect twin: 0.200)

after pointless and merging with aimless:
  Mean |L|   :0.492  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.322  (untwinned: 0.333; perfect twin: 0.200)

As workaround, run the data through pointless/aimless first.

Best,
Tim

On 07/03/2014 05:04 AM, Yamei Yu wrote:
 HI all,
 
I have a data set processed to P42 21 2 (the space group was suggested by 
 pointless ). then I use phenix.xtriage to analysis the data. I was confused 
 by the phenix.xtriage result.  
 According to the following number it is twin data, but why it couldn’t find 
 any possible twin law?
 
 Determining possible twin laws.
 
   0 merohedral twin operators found
   0 pseudo-merohedral twin operators found
 In total,   0 twin operator were found
 
 
  Mean |L|   :0.378  (untwinned: 0.500; perfect twin: 0.375)
   Mean  L^2  :0.205  (untwinned: 0.333; perfect twin: 0.200)
 
 
 How could be that? Is it twin or no twin?
 
 Please find the log file of phenix.xtrage in attachment. 
 
 Thank you so much for your suggestion!
 
 
 
 
 Yamei Yu
 
 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] twin or untwinned

[Dirk Kostrewa]

... and please check, whether phenix.xtriage recognized the input data 
as intensities or as amplitudes.
In case of doubt, convert the intensives first into an mtz file with Fs 
instead of Is and run phenix.xtriage on the mtz file.


Best regards,

Dirk.

Am 03.07.2014 13:36, schrieb Tim Gruene:

Hi Yamei,

did you by any chance feed the output file from XDS into xtriage? It
would indicate the data were twinned even for a near perfect insulin
test crystal. After discussion with the developers I understand that
phenix does not seem to handle unmerged data well.

With phenix.xtriage V. phenix-1.9-1692:, XDS_ASCII.HKL
   Mean |L|   :0.392  (untwinned: 0.500; perfect twin: 0.375)
   Mean  L^2  :0.219  (untwinned: 0.333; perfect twin: 0.200)

after pointless and merging with aimless:
   Mean |L|   :0.492  (untwinned: 0.500; perfect twin: 0.375)
   Mean  L^2  :0.322  (untwinned: 0.333; perfect twin: 0.200)

As workaround, run the data through pointless/aimless first.

Best,
Tim

On 07/03/2014 05:04 AM, Yamei Yu wrote:

HI all,

I have a data set processed to P42 21 2 (the space group was suggested by 
pointless ). then I use phenix.xtriage to analysis the data. I was confused by 
the phenix.xtriage result.
According to the following number it is twin data, but why it couldn’t find any 
possible twin law?

Determining possible twin laws.

   0 merohedral twin operators found
   0 pseudo-merohedral twin operators found
In total,   0 twin operator were found


  Mean |L|   :0.378  (untwinned: 0.500; perfect twin: 0.375)
   Mean  L^2  :0.205  (untwinned: 0.333; perfect twin: 0.200)


How could be that? Is it twin or no twin?

Please find the log file of phenix.xtrage in attachment.

Thank you so much for your suggestion!




Yamei Yu




--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] twin or untwinned

[Tim Gruene]

Hi Dirk,

that would truely be very sad - the XDS file format is such a beautiful,
self-contained and well documented format for diffraction data that a
misinterpretation should really not happen.

Cheers,
Tim

On 07/03/2014 01:42 PM, Dirk Kostrewa wrote:
 ... and please check, whether phenix.xtriage recognized the input data
 as intensities or as amplitudes.
 In case of doubt, convert the intensives first into an mtz file with Fs
 instead of Is and run phenix.xtriage on the mtz file.
 
 Best regards,
 
 Dirk.
 
 Am 03.07.2014 13:36, schrieb Tim Gruene:
 Hi Yamei,

 did you by any chance feed the output file from XDS into xtriage? It
 would indicate the data were twinned even for a near perfect insulin
 test crystal. After discussion with the developers I understand that
 phenix does not seem to handle unmerged data well.

 With phenix.xtriage V. phenix-1.9-1692:, XDS_ASCII.HKL
Mean |L|   :0.392  (untwinned: 0.500; perfect twin: 0.375)
Mean  L^2  :0.219  (untwinned: 0.333; perfect twin: 0.200)

 after pointless and merging with aimless:
Mean |L|   :0.492  (untwinned: 0.500; perfect twin: 0.375)
Mean  L^2  :0.322  (untwinned: 0.333; perfect twin: 0.200)

 As workaround, run the data through pointless/aimless first.

 Best,
 Tim

 On 07/03/2014 05:04 AM, Yamei Yu wrote:
 HI all,

 I have a data set processed to P42 21 2 (the space group was
 suggested by pointless ). then I use phenix.xtriage to analysis the
 data. I was confused by the phenix.xtriage result.
 According to the following number it is twin data, but why it
 couldn’t find any possible twin law?

 Determining possible twin laws.

0 merohedral twin operators found
0 pseudo-merohedral twin operators found
 In total,   0 twin operator were found


   Mean |L|   :0.378  (untwinned: 0.500; perfect twin: 0.375)
Mean  L^2  :0.205  (untwinned: 0.333; perfect twin: 0.200)


 How could be that? Is it twin or no twin?

 Please find the log file of phenix.xtrage in attachment.

 Thank you so much for your suggestion!


 

 Yamei Yu


 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] twin or untwinned

[Dirk Kostrewa]

Hi Tim,

yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL 
intensities as amplitudes, producing very different output statistics, 
compared both to the XDS statistics and to an mtz file with amplitudes 
created from that XDS file. I've contacted a phenix developer a few 
weeks ago, but got no reply, yet (maybe, my e-mail got lost).


Cheers,

Dirk.

Am 03.07.2014 13:46, schrieb Tim Gruene:

Hi Dirk,

that would truely be very sad - the XDS file format is such a beautiful,
self-contained and well documented format for diffraction data that a
misinterpretation should really not happen.

Cheers,
Tim

On 07/03/2014 01:42 PM, Dirk Kostrewa wrote:

... and please check, whether phenix.xtriage recognized the input data
as intensities or as amplitudes.
In case of doubt, convert the intensives first into an mtz file with Fs
instead of Is and run phenix.xtriage on the mtz file.

Best regards,

Dirk.

Am 03.07.2014 13:36, schrieb Tim Gruene:

Hi Yamei,

did you by any chance feed the output file from XDS into xtriage? It
would indicate the data were twinned even for a near perfect insulin
test crystal. After discussion with the developers I understand that
phenix does not seem to handle unmerged data well.

With phenix.xtriage V. phenix-1.9-1692:, XDS_ASCII.HKL
Mean |L|   :0.392  (untwinned: 0.500; perfect twin: 0.375)
Mean  L^2  :0.219  (untwinned: 0.333; perfect twin: 0.200)

after pointless and merging with aimless:
Mean |L|   :0.492  (untwinned: 0.500; perfect twin: 0.375)
Mean  L^2  :0.322  (untwinned: 0.333; perfect twin: 0.200)

As workaround, run the data through pointless/aimless first.

Best,
Tim

On 07/03/2014 05:04 AM, Yamei Yu wrote:

HI all,

 I have a data set processed to P42 21 2 (the space group was
suggested by pointless ). then I use phenix.xtriage to analysis the
data. I was confused by the phenix.xtriage result.
According to the following number it is twin data, but why it
couldn’t find any possible twin law?

Determining possible twin laws.

0 merohedral twin operators found
0 pseudo-merohedral twin operators found
In total,   0 twin operator were found


   Mean |L|   :0.378  (untwinned: 0.500; perfect twin: 0.375)
Mean  L^2  :0.205  (untwinned: 0.333; perfect twin: 0.200)


How could be that? Is it twin or no twin?

Please find the log file of phenix.xtrage in attachment.

Thank you so much for your suggestion!




Yamei Yu




--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] twin or untwinned

[Nat Echols]

On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de
wrote:

 yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
 intensities as amplitudes, producing very different output statistics,
 compared both to the XDS statistics and to an mtz file with amplitudes
 created from that XDS file.


This is incorrect.  It does read it correctly as intensities - the
confusion probably arises from the fact that Xtriage internally converts
everything to amplitudes immediately, so that when it reports the summary
of file information, it will say xray.amplitude no matter what the input
type was (the same will also be true for Scalepack and MTZ formats).
However, the data will be converted back to intensities as needed for the
individual analyses.  Obviously this isn't quite ideal either since the
original intensities are preferable but for the purpose of detecting
twinning I hope it will be okay.  In any case the incorrect feedback
confused several other users so it's gone as of a few weeks ago, and the
current nightly builds will report the true input data type.  (The actual
results are unchanged.)

Tim: I have no reason to think we handle unmerged data poorly; I'm not sure
who would have told you that.  In most cases they will be merged as needed
upon reading the file.  I'm a little concerned that you're getting such
different results from Xtriage and pointless/aimless, however.  Could you
please send me the input and log files off-list?  Dirk, same thing: if you
have an example where XDS and Xtriage are significantly in disagreement,
the inputs (and logs) would be very helpful.  In both cases, I suspect the
difference is in the use of resolution cutoffs and absolute-scaled
intensities in Xtriage versus other programs, but I'd like to be certain
that there's not something broken.

thanks,
Nat

Re: [ccp4bb] Twin refinement in Refmac

[Garib Murshudov]

Dear Uli,

It seems that you are dealing with psued-twinning when cell do not overlap 
after rotation with twin operator. In these case what is in one resolution on 
one of the orientation becomes another resolution in another orientation of 
crystals

In short:. You have an operator R that relates two orientation of the crystal. 
If R does not convert cell to itself completely then resolution of twin related 
reflections h' and h 

h' = Rh


will be different. It usually means that in your images spots are split at 
higher resolution. If you have not integrated those spots as one at higher 
resolution then refinement may not be optimal. These cases needs to be 
considered as multiple orientation of the same crystal. I think MOSFLM should 
be able to integrate them as several cells. However refmac is not completely 
ready to deal with these cases as optimally as it should.

I hope it clears things a bit.

Cheers,
Garib



On 22 May 2014, at 15:48, ulrich.goh...@mdc-berlin.de 
ulrich.goh...@mdc-berlin.de wrote:

 Dear colleagues,
 
  I am in the process of refining a P2(1) structure that is marked by Scala as 
 twinned (L-test etc.) with a twinning fraction of ca. 0.2. I am still working 
 on the twinning problem, so no more details about this. But what puzzles me 
 right now is that, if I feed the data with a max. resolution of 1.95 A into 
 Refmac with the twin refinement option on, it recognizes the resolution 
 cut-off at first, but then uses a new cut-off  of 1.88 A in the first ( and 
 all subsequent) refinement cycles. Since there are no data at this 
 resolution, this seems to screw up the calculation of R-values at high 
 resolution and it reports for them zero-values in the co-ordinate header. 
 Without twin refinement, the max. resolution stays at 1.95 A (but the final 
 stats are worse, of course). 
 
 Is this a bug or am I missing here something?
 
 Thanks in advance, and I am happy to send log files or my precious data if 
 necessary.
 
 Cheers,
 
  Uli
 
 ---
 dr ulrich gohlke
 staff scientist - macromolecular structure and interaction
 max-delbrück-center for molecular medicine (mdc)
 
 +49 30 9406 - 2725 (w)
 +49 30 9406 - 2548 (fax)
 ulrich.goh...@mdc-berlin.de
  
 http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/

Dr Garib N Murshudov
MRC-LMB
Francis Crick Avenue
Cambridge 
CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk, 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/

Re: [ccp4bb] Twin refinement in Refmac

[Ulrich Gohlke]

Dear Garib,

 thanks for the clarification. I'll go back to the raw data and check for split 
spots at high resolution (and give Mosflm a try; initially, the data were 
integrated with XDS).

Cheers,

 Uli

---
dr ulrich gohlke
staff scientist - macromolecular structure and interaction
max-delbrück-center for molecular medicine (mdc)

+49 30 9406 - 2725 (w)
+49 30 9406 - 2548 (fax)
ulrich.goh...@mdc-berlin.de
 
http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/

Re: [ccp4bb] twin refinement

[Eleanor Dodson]

If the twin law is k,h,-l, then your a axis must almost equal the b axis?
And if the twin fraction is 0.48 then you have additional symmetry I guess?

How sure are you that the point group is P4/mmm?




On 13 March 2014 20:41, Teresa Swanson teresa.m.swan...@gmail.com wrote:

 Dear collegues,

 I'm working with a drug complexed protein structure that is having major
 twinning issues. The drug has a single Br atom on a benzene ring, which I'd
 like to use for orienting the drug in the binding site.  I have various
 anomalous data sets, ranging from 3.0A resolution, all scaled into P222
 with a Rlin of .125.

 Using MR, the twin law (k, h, -l) and NCS restraints, I can confidently
 solve the structure without anomalous, and the drug density is clear in the
 Fo-Fc map, with Rw/Rf at ~.26/.29 and a space group of P21221. It might be
 important to note that any simulated annealing I've tried invariably
 increases the Rfree by 2-3%, so I've scraped it. As you can imagine, when
 using the twinned data, the anomalous maps are weak and random.

 I've used the Phenix detwin option in Xtriage to see if I can pull the
 anomalous signal out of it. If I use the .mtz file that is output for MR
 and calculate the anomalous maps, it looks promising. The twin fraction for
 the one particular dataset I've been using is estimated at approx .48. Is
 this too close to 50% to do the detwinning? Now I'm wondering how to
 properly refine this further. I'm assuming that since I've detwinned the
 data, I do refinement without the twin law. But that gives an initial Rf of
 .38 when using it gives .31.  Since I've already solved the structure
 without using the anomalous flag, can I just use the detwinned
 reflections and the refined structure to calculate an anomalous map
 (without having to redo the refinement)?

 Mainly, my main question is about how to tease out and properly refine the
 anomalous data from a twinned structure. Also, how much of a difference
 will it make to scale into P222 versus P21212. And, if I have quite high
 redundancy, should I scale anomalous in HKL2000 or just use the
 anomalous flag?

 Any help on refining this twinned structure would be greatly appreciated!
 Thanks,

 Teresa
 PhD Student

Re: [ccp4bb] twin refinement

[Jon Schuermann]

Hi Teresa,

   As Eleanor has mentioned, you should probably check out other space 
groups. Xtriage gives a lot of great information and many plots to 
inspect. But, if you do not know what the plots mean and just look at 
the results that say the twin fraction is 0.48 you can get into some 
trouble. From what I have seen over the years, when most people say they 
have a twin fraction nearly 0.5, they are usually in the wrong space 
group and the data is not twinned. When the summary table shows a low 'R 
obs' and a high twin fraction across the tests that means that the 
operator is present in the data. But that could be a crystallographic 
operator or a twin operator. You would have to inspect the plots to see 
if the data looks twinned, but if there is pseudosymmetry it could make 
the plots look not twinned. You could run the extra twin tests in 
Xtriage inputting the MR solution so that the R vs. R plot (Andrey 
Lebedev, et al. (2006) , Acta Crystallogr. D62, 83-95) could be 
calculated. In the end, your data could be nearly perfectly twinned, I 
have had it happen a couple of times, but I always tell people to assume 
it is not until the model building is done and the R-factor still won't 
drop. Your R-factors are not that bad for 3A resolution, indicating the 
operator might be crystallographic and you are too low in symmetry.


   So if you have done all this and you still believe the data is 
twinned... Don't detwin your data! Your twin fraction is too high and it 
will introduce a lot of errors. This has been gone over many times and 
you can search the archives. I never detwin data regardless of twin 
fraction. Modern programs like Phenix.refine and Refmac (I think) handle 
twinned data just fine. If you are just trying to calculate an ADF map 
to find the Br then it might be difficult since the peak heights are 
going to be lower. Your best bet is to increase your redundancy without 
killing the crystal with too much radiation damage. If your redundancy 
is around 10 or so then you could probably use the 'scale anomalous' 
option. I tend to scale with and without it and look at the maps to see 
if it helps or not. Sometimes it helps, other times it doesn't and I am 
sure there are reasons (like anisotropy). Another word of caution is the 
possibility of model bias in the maps when the twin fraction approaches 
0.5. The programs will use the model in the detwinning process if the 
twin fraction is above a certain threshold. I believe it is 0.45 in 
Phenix.refine.


First thing I would do is follow Eleanor's lead and check out other 
space groups. You might have pseudo-symmetry with or without twinning.


Jon

--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist, NE-CAT
Argonne National Laboratory, 436E
9700 S. Cass Ave.
Argonne, IL 60439

Email: schue...@anl.gov
Tel: (630) 252-0682


On 03/13/2014 03:41 PM, Teresa Swanson wrote:

Dear collegues,

I'm working with a drug complexed protein structure that is having major 
twinning issues. The drug has a single Br atom on a benzene ring, which I'd 
like to use for orienting the drug in the binding site.  I have various 
anomalous data sets, ranging from 3.0A resolution, all scaled into P222 with a 
Rlin of .125.

Using MR, the twin law (k, h, -l) and NCS restraints, I can confidently solve 
the structure without anomalous, and the drug density is clear in the Fo-Fc 
map, with Rw/Rf at ~.26/.29 and a space group of P21221. It might be important 
to note that any simulated annealing I've tried invariably increases the Rfree 
by 2-3%, so I've scraped it. As you can imagine, when using the twinned data, 
the anomalous maps are weak and random.

I've used the Phenix detwin option in Xtriage to see if I can pull the anomalous signal out of 
it. If I use the .mtz file that is output for MR and calculate the anomalous maps, it looks promising. The 
twin fraction for the one particular dataset I've been using is estimated at approx .48. Is this too close to 
50% to do the detwinning? Now I'm wondering how to properly refine this further. I'm assuming that since I've 
detwinned the data, I do refinement without the twin law. But that gives an initial Rf of .38 
when using it gives .31.  Since I've already solved the structure without using the anomalous flag, can I 
just use the detwinned reflections and the refined structure to calculate an anomalous map 
(without having to redo the refinement)?

Mainly, my main question is about how to tease out and properly refine the anomalous data from a 
twinned structure. Also, how much of a difference will it make to scale into P222 versus P21212. 
And, if I have quite high redundancy, should I scale anomalous in HKL2000 or just use 
the anomalous flag?

Any help on refining this twinned structure would be greatly appreciated!
Thanks,

Teresa
PhD Student



--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist, NE-CAT
Argonne National Laboratory, 436E
9700 S. Cass Ave.
Argonne, IL 60439

Email: schue...@anl.gov
Tel: 

Re: [ccp4bb] twin refinement

[Robbie Joosten]

Dear Wolfram,

First of all you should make sure you have substantial twinning. Is the twin 
fraction close to zero, then don't use a twin target. Is twinning detected by 
several test, then there is a good chance your data are twinned.
As for validation, if you do not completely trust your R-factors or maps, spend 
more time looking at geometry. That is independent of your diffraction data, 
but still a very good way to see whether your model is plausible.

Hth,
Robbie

Sent from my Windows Phone

Van: wtempel
Verzonden: 13-3-2014 15:19
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] twin refinement

Dear colleagues,

this is a request for comments on the evaluation of crystal structures that
resulted from twin refinement.

From http://www.ysbl.york.ac.uk/~garib/refmac/Tutorials/refmac_tutorial.pdf:

Although Rfactors are substantially smaller with twin refinement than
without twin
refinement it does not mean that model also is substantially better.
[...]
Usually twin maps after twin refinement are more biased
towards errors in the model.

From phenix.xtriage output:

Please note however that R-factors from twinned refinement cannot be
directly
compared to R-factors without twinning, as they will always be lower when a
twin law is used.  You should also use caution when interpreting the maps
from
refinement, as they will have significantly more model bias.

How would you ascertain that inclusion of twin parameters has improved the
model?
How is one to judge the evidentiary strength of such crystal structure in
general, given that validation by residuals and maps is further weakened
compared to refinement without twinning parameters?

Thank you for your thoughts and time,
Wolfram Tempel

Re: [ccp4bb] Twin or underestimation of symmetry

[Eleanor Dodson]

This is a bit puzzling.
Sticking to point groups:
P3   P6 are sub groups of P6/mmm so data which merges in P6/mmm will
always satisfy P3 and P6.
And twinning in P3 or P6 will make the data seem to have higher symmetry.
Four way twinning is unusual, but possible of course.

But if you really have twinning, you should see it indicated in the
pointless/aimless plots, or via Xtriage.. If those tests do not show it and
you dont have a non-crystallographic translation twinning is unlikely.

Your choice of SGs seem puzzling too.
 If the data is P31 (or P32) then you should see intensities for l=3n, and
absences for l=3n+-1
If the data is P61 (or P65) then you should only see intensities for l=6n.
If the data is P6322 you should only see intensities for l=2n.
What are the absences along 00l?

Eleanor






On 29 July 2013 18:37, Jeffrey D Brodin jbro...@ucsd.edu wrote:

  Hi everyone,

 I have a dataset that's been giving me some trouble and wanted to get your
 ideas on the best way to proceed. The data extend to ~2.6 Å and scale
 integrate/scale well in P622. According to Pointless, the symmetry is
 either P622 or P6322, however, neither Molrep norm Phaser finds molecular
 replacement solutions in these space groups. If I run Phaser and let it
 check all other space groups it finds a solution in P6122, but I can only
 refine it to an Rfree value of ~35%. The data also scales well in P3 and P6
 and I get molecular replacement solutions in space groups of either P31 or
 P61. However, the Refinement again stalls at an Rfree value of ~35%. I
 tried adding twin refinement in Refmac and it seems to be helping; The
 R/Rfree values dropped to 20.9/27.3 and the map appears much better
 compared to the previous refinements. The refined twin fractions are 0.26,
 0.24, 0.24 and 0.25. Am I doing something wrong with the refinement or is
 this a legitimate way to treat the data. Thank you in advance for your help.
 *
 *

Re: [ccp4bb] Twin or underestimation of symmetry

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jeffrey,

how complete is you model, i.e. what is the ratio between  the number
of atoms in the PDB file (without solvent/ ligands) and the expected
number of atoms as calculated from the sequence?
If a substantial part of the molecule is disordered you may not be
able to get a much better model.

What is the R-value and Rfree? If you have placed many water atoms you
may have hovered out the difference density allowing you to further
improve your model.

Regards,
Tim

On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote:
 Hi everyone,
 
 I have a dataset that's been giving me some trouble and wanted to
 get your ideas on the best way to proceed. The data extend to ~2.6
 Å and scale integrate/scale well in P622. According to Pointless,
 the symmetry is either P622 or P6322, however, neither Molrep norm
 Phaser finds molecular replacement solutions in these space groups.
 If I run Phaser and let it check all other space groups it finds a
 solution in P6122, but I can only refine it to an Rfree value of
 ~35%. The data also scales well in P3 and P6 and I get molecular
 replacement solutions in space groups of either P31 or P61.
 However, the Refinement again stalls at an Rfree value of ~35%. I
 tried adding twin refinement in Refmac and it seems to be helping;
 The R/Rfree values dropped to 20.9/27.3 and the map appears much
 better compared to the previous refinements. The refined twin
 fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong
 with the refinement or is this a legitimate way to treat the data.
 Thank you in advance for your help.
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.14 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFR97DoUxlJ7aRr7hoRAsfrAKCIEYpOkrVfm/VrkIn+Jn9NZ16swACguGLe
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Re: [ccp4bb] Twin or underestimation of symmetry

[Phoebe A. Rice]

Check the pseudo-precession pics (0kl plane, etc).  A rhombohedral crystal that 
is indexed as P6xx may have seemingly-bizarre systematic absences that could 
trick one into thinking its P63xx.  

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Sent: Tuesday, July 30, 2013 7:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Twin or underestimation of symmetry

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jeffrey,

how complete is you model, i.e. what is the ratio between  the number
of atoms in the PDB file (without solvent/ ligands) and the expected
number of atoms as calculated from the sequence?
If a substantial part of the molecule is disordered you may not be
able to get a much better model.

What is the R-value and Rfree? If you have placed many water atoms you
may have hovered out the difference density allowing you to further
improve your model.

Regards,
Tim

On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote:
 Hi everyone,

 I have a dataset that's been giving me some trouble and wanted to
 get your ideas on the best way to proceed. The data extend to ~2.6
 Å and scale integrate/scale well in P622. According to Pointless,
 the symmetry is either P622 or P6322, however, neither Molrep norm
 Phaser finds molecular replacement solutions in these space groups.
 If I run Phaser and let it check all other space groups it finds a
 solution in P6122, but I can only refine it to an Rfree value of
 ~35%. The data also scales well in P3 and P6 and I get molecular
 replacement solutions in space groups of either P31 or P61.
 However, the Refinement again stalls at an Rfree value of ~35%. I
 tried adding twin refinement in Refmac and it seems to be helping;
 The R/Rfree values dropped to 20.9/27.3 and the map appears much
 better compared to the previous refinements. The refined twin
 fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong
 with the refinement or is this a legitimate way to treat the data.
 Thank you in advance for your help.


- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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=q8Ki
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Re: [ccp4bb] Twin or underestimation of symmetry

[Jeffrey D Brodin]

The model is essentially 100% identical. The structure is of a point mutant 
that has already been solved.


From: Tim Gruene [t...@shelx.uni-ac.gwdg.de]
Sent: Tuesday, July 30, 2013 5:26 AM
To: Jeffrey D Brodin
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Twin or underestimation of symmetry

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jeffrey,

how complete is you model, i.e. what is the ratio between  the number
of atoms in the PDB file (without solvent/ ligands) and the expected
number of atoms as calculated from the sequence?
If a substantial part of the molecule is disordered you may not be
able to get a much better model.

What is the R-value and Rfree? If you have placed many water atoms you
may have hovered out the difference density allowing you to further
improve your model.

Regards,
Tim

On 07/29/2013 07:37 PM, Jeffrey D Brodin wrote:
 Hi everyone,

 I have a dataset that's been giving me some trouble and wanted to
 get your ideas on the best way to proceed. The data extend to ~2.6
 Å and scale integrate/scale well in P622. According to Pointless,
 the symmetry is either P622 or P6322, however, neither Molrep norm
 Phaser finds molecular replacement solutions in these space groups.
 If I run Phaser and let it check all other space groups it finds a
 solution in P6122, but I can only refine it to an Rfree value of
 ~35%. The data also scales well in P3 and P6 and I get molecular
 replacement solutions in space groups of either P31 or P61.
 However, the Refinement again stalls at an Rfree value of ~35%. I
 tried adding twin refinement in Refmac and it seems to be helping;
 The R/Rfree values dropped to 20.9/27.3 and the map appears much
 better compared to the previous refinements. The refined twin
 fractions are 0.26, 0.24, 0.24 and 0.25. Am I doing something wrong
 with the refinement or is this a legitimate way to treat the data.
 Thank you in advance for your help.


- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Re: [ccp4bb] twin refinement in refmac

[Eleanor Dodson]

Is this twinning or several crystals indexed according to different 
conventions? You usually see evidence of twinning for each crystal if it is 
really there..


Trigonal data can be indexed as h,k,l k,h,-k -h,-k,l or -k,-h,-l of course 
so you have a 75% chance of getting the 2nd crystal on a different 
convention than the first.. POINTLESS checks for this if you give it pairs 
of input files and does a good job in selecting the same indexing 
convention - providing of course the twinning isnt present.


I would be suspicious because

a) I have been convinced by having more than 2 twin domains b) when there 
is twinning the data analysis on each crystal seperately shows it up.


Eleanor

- On Mar 2 2012, wtempel wrote:


Dear CCp4ers,
A good morning to everyone.
Today, I have a structure that I initially refined in space group P6522,
1mol/asu.
Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
2.61-2.55A: Rsym=39.6%, I/sigma  10
50.00-6.13: Rsym=6.4%
Some mild anisotropy in the resolution limits is apparent on the
diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in
the other.
Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A
resolution, with some difference density for loops that cannot be
interpreted with reasonable geometry.
Rsym is very similar for data scaled in P3, in all resolution shells.
Xtriage does not suggest merohedral twinning.
Nevertheless, I extended my free flags in sftools from P6522 to P32 and
cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I
expanded my model to a homotetramer and ran Refmac with amplitude based
twinning. (Would this be a reasonable input to twin refinement?)
From the output coordinates:
REMARK   3  TWIN DETAILS
REMARK   3   NUMBER OF TWIN DOMAINS  :4
REMARK   3  TWIN DOMAIN   :1
REMARK   3  TWIN OPERATOR :  H,  K,  L
REMARK   3  TWIN FRACTION : 0.269
REMARK   3  TWIN DOMAIN   :2
REMARK   3  TWIN OPERATOR : -K, -H, -L
REMARK   3  TWIN FRACTION : 0.171
REMARK   3  TWIN DOMAIN   :3
REMARK   3  TWIN OPERATOR :  K,  H, -L
REMARK   3  TWIN FRACTION : 0.258
REMARK   3  TWIN DOMAIN   :4
REMARK   3  TWIN OPERATOR : -H, -K,  L
REMARK   3  TWIN FRACTION : 0.302
Does this establish twinning versus underestimated symmetry? And what do I
need to know about my free-R? Did refmac assign a new flag? Whereas the
output file's flags are all 1s and 0s, the input file had 0 ... 19. During
the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was
stuck 30% when I used the initial job's output MTZ.
Many thanks in advance for your helpful comments.
Wolfram Tempel



--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266

Re: [ccp4bb] twin refinement in refmac

[arka chakraborty]

Hi all,

I will like to know, as a follow up of what Prof. Randy Read said, what
should be done to do the refinement against the measured data and not the
detwinned F( which refmac outputs in the mtz after twin refinement), during
subsequent refinements. And also, I would like to know how to ensure that
the free R generated takes twinning into account if I am not using phenix.

Thanks in advance,

Regards,

ARKO

On Fri, Mar 2, 2012 at 12:44 PM, Randy J. Read rj...@cam.ac.uk wrote:

 I'm worried when you say that you use the initial job's output MTZ. Refmac
 replaces F with a detwinned F in the output file so you wouldn't be
 refining against your measured data in the subsequent round.

 Best wishes

 Randy Read

 
 Randy J. Read

 On 2 Mar 2012, at 02:00, wtempel wtem...@gmail.com wrote:

  Dear CCp4ers,
  A good morning to everyone.
  Today, I have a structure that I initially refined in space group P6522,
 1mol/asu.
  Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
  2.61-2.55A: Rsym=39.6%, I/sigma  10
  50.00-6.13: Rsym=6.4%
  Some mild anisotropy in the resolution limits is apparent on the
 diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in
 the other.
  Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like
 3.5A resolution, with some difference density for loops that cannot be
 interpreted with reasonable geometry.
  Rsym is very similar for data scaled in P3, in all resolution shells.
 Xtriage does not suggest merohedral twinning.
  Nevertheless, I extended my free flags in sftools from P6522 to P32 and
 cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I
 expanded my model to a homotetramer and ran Refmac with amplitude based
 twinning. (Would this be a reasonable input to twin refinement?)
  From the output coordinates:
  REMARK   3  TWIN DETAILS
  REMARK   3   NUMBER OF TWIN DOMAINS  :4
  REMARK   3  TWIN DOMAIN   :1
  REMARK   3  TWIN OPERATOR :  H,  K,  L
  REMARK   3  TWIN FRACTION : 0.269
  REMARK   3  TWIN DOMAIN   :2
  REMARK   3  TWIN OPERATOR : -K, -H, -L
  REMARK   3  TWIN FRACTION : 0.171
  REMARK   3  TWIN DOMAIN   :3
  REMARK   3  TWIN OPERATOR :  K,  H, -L
  REMARK   3  TWIN FRACTION : 0.258
  REMARK   3  TWIN DOMAIN   :4
  REMARK   3  TWIN OPERATOR : -H, -K,  L
  REMARK   3  TWIN FRACTION : 0.302
  Does this establish twinning versus underestimated symmetry? And what do
 I need to know about my free-R? Did refmac assign a new flag? Whereas the
 output file's flags are all 1s and 0s, the input file had 0 ... 19. During
 the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was
 stuck 30% when I used the initial job's output MTZ.
  Many thanks in advance for your helpful comments.
  Wolfram Tempel
 




-- 

*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*

Re: [ccp4bb] twin refinement in refmac

[Randy Read]

Garib may have more to say, but the first point would be to always include the 
original data file as your input MTZ file for any cycle of refinement, whether 
you're using Refmac in CCP4 or phenix.refine.  (In phenix.refine, if you assign 
the R-free data the first time you do refinement, it will produce a file 
containing all the information used in that cycle of refinement, including the 
new R-free flags and possibly any Hendrickson-Lattman coefficients, and you 
should use that file for all subsequent refinements.)

As for whether R-free takes twinning into account, I think it's fair to say 
that all the refinement programs that handle twinning will do this 
appropriately.

Regards,

Randy Read

On 2 Mar 2012, at 08:01, arka chakraborty wrote:

 Hi all,
 
 I will like to know, as a follow up of what Prof. Randy Read said, what 
 should be done to do the refinement against the measured data and not the 
 detwinned F( which refmac outputs in the mtz after twin refinement), during 
 subsequent refinements. And also, I would like to know how to ensure that the 
 free R generated takes twinning into account if I am not using phenix.
 
 Thanks in advance,
 
 Regards,
 
 ARKO
 
 On Fri, Mar 2, 2012 at 12:44 PM, Randy J. Read rj...@cam.ac.uk wrote:
 I'm worried when you say that you use the initial job's output MTZ. Refmac 
 replaces F with a detwinned F in the output file so you wouldn't be refining 
 against your measured data in the subsequent round.
 
 Best wishes
 
 Randy Read
 
 
 Randy J. Read
 
 On 2 Mar 2012, at 02:00, wtempel wtem...@gmail.com wrote:
 
  Dear CCp4ers,
  A good morning to everyone.
  Today, I have a structure that I initially refined in space group P6522, 
  1mol/asu.
  Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
  2.61-2.55A: Rsym=39.6%, I/sigma  10
  50.00-6.13: Rsym=6.4%
  Some mild anisotropy in the resolution limits is apparent on the 
  diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in 
  the other.
  Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A 
  resolution, with some difference density for loops that cannot be 
  interpreted with reasonable geometry.
  Rsym is very similar for data scaled in P3, in all resolution shells. 
  Xtriage does not suggest merohedral twinning.
  Nevertheless, I extended my free flags in sftools from P6522 to P32 and 
  cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I 
  expanded my model to a homotetramer and ran Refmac with amplitude based 
  twinning. (Would this be a reasonable input to twin refinement?)
  From the output coordinates:
  REMARK   3  TWIN DETAILS
  REMARK   3   NUMBER OF TWIN DOMAINS  :4
  REMARK   3  TWIN DOMAIN   :1
  REMARK   3  TWIN OPERATOR :  H,  K,  L
  REMARK   3  TWIN FRACTION : 0.269
  REMARK   3  TWIN DOMAIN   :2
  REMARK   3  TWIN OPERATOR : -K, -H, -L
  REMARK   3  TWIN FRACTION : 0.171
  REMARK   3  TWIN DOMAIN   :3
  REMARK   3  TWIN OPERATOR :  K,  H, -L
  REMARK   3  TWIN FRACTION : 0.258
  REMARK   3  TWIN DOMAIN   :4
  REMARK   3  TWIN OPERATOR : -H, -K,  L
  REMARK   3  TWIN FRACTION : 0.302
  Does this establish twinning versus underestimated symmetry? And what do I 
  need to know about my free-R? Did refmac assign a new flag? Whereas the 
  output file's flags are all 1s and 0s, the input file had 0 ... 19. During 
  the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was 
  stuck 30% when I used the initial job's output MTZ.
  Many thanks in advance for your helpful comments.
  Wolfram Tempel
 
 
 
 
 -- 
 
 ARKA CHAKRABORTY
 CAS in Crystallography and Biophysics
 University of Madras
 Chennai,India
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] twin refinement in refmac

[Garib N Murshudov]

1) You should use measured data (after scala/aimless/truncate). In general 
there may not be one to one relationship between observed data and asymmetric 
unit (e.g. non-merohedral twinning) and it would not be possible to bring input 
data to output file. Use original data
2) Internally refmac groups reflection into classes. All twin related 
reflections belong to one class. In the example you give four reflections 
belong to one class. FreeR is property of the class not individual relfections. 
I.e. all twin related reflections belong either to free or working class. If 
your input data has this property then output should also have this. In the 
output file there will be 0 (for free) and 1 (working)
3) At early stages it is not easy to factorise twin and underestimated 
symmetry. It seems that L-test is the best way of making decision if you 
crystals are twinnined. If you collect data from many crystals and merge them 
then you artificially twin (or increase twinning). Using pointless to index all 
datasets consistently may sort some of the problems 
4) In this case it seems that you may need to reindex. Largest twin domain is 
not the first one

Regards
Garib


On 2 Mar 2012, at 02:00, wtempel wrote:

 Dear CCp4ers,
 A good morning to everyone.
 Today, I have a structure that I initially refined in space group P6522, 
 1mol/asu.
 Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
 2.61-2.55A: Rsym=39.6%, I/sigma  10
 50.00-6.13: Rsym=6.4%
 Some mild anisotropy in the resolution limits is apparent on the diffraction 
 images. Say, visible spots at 2.2A in one direction, 2.6A in the other.
 Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A 
 resolution, with some difference density for loops that cannot be interpreted 
 with reasonable geometry.
 Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage 
 does not suggest merohedral twinning.
 Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad'd 
 them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my 
 model to a homotetramer and ran Refmac with amplitude based twinning. (Would 
 this be a reasonable input to twin refinement?)
 From the output coordinates:
 REMARK   3  TWIN DETAILS
 REMARK   3   NUMBER OF TWIN DOMAINS  :4
 REMARK   3  TWIN DOMAIN   :1
 REMARK   3  TWIN OPERATOR :  H,  K,  L
 REMARK   3  TWIN FRACTION : 0.269
 REMARK   3  TWIN DOMAIN   :2
 REMARK   3  TWIN OPERATOR : -K, -H, -L
 REMARK   3  TWIN FRACTION : 0.171
 REMARK   3  TWIN DOMAIN   :3
 REMARK   3  TWIN OPERATOR :  K,  H, -L
 REMARK   3  TWIN FRACTION : 0.258
 REMARK   3  TWIN DOMAIN   :4
 REMARK   3  TWIN OPERATOR : -H, -K,  L
 REMARK   3  TWIN FRACTION : 0.302
 Does this establish twinning versus underestimated symmetry? And what do I 
 need to know about my free-R? Did refmac assign a new flag? Whereas the 
 output file's flags are all 1s and 0s, the input file had 0 ... 19. During 
 the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was 
 stuck 30% when I used the initial job's output MTZ.
 Many thanks in advance for your helpful comments.
 Wolfram Tempel
 

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] twin refinement in refmac

[Steiner, Roberto]

On 2 Mar 2012, at 08:01, arka chakraborty wrote:

Hi all,

I will like to know, as a follow up of what Prof. Randy Read said, what should 
be done to do the refinement against the measured data and not the detwinned F( 
which refmac outputs in the mtz after twin refinement), during subsequent 
refinements.

Operationally, don't put in the MTZ in field of the GUI something that Refmac 
generated for you in a previous run as MTZ out file. Always use as MTZ in 
your original data file.

And also, I would like to know how to ensure that the free R generated takes 
twinning into account if I am not using phenix.

Refmac does take in consideration the twin law(s) when handling free 
reflections . This is the case even if you have generated your free reflections 
randomly. Internally Refmac will modify your Free set in such a way that twin 
related reflections are in the same group (free or working) -- classes 
mentioned by Garib

The good thing about this is that twin-related reflections are handled properly 
during refinement irrespective of your Free-set choice.
The bad thing (Garib please correct me if I am wrong here) is that you might 
end up depositing a Free set which is not that actually used in refinement.

Best wishes
Roberto



Thanks in advance,

Regards,

ARKO

On Fri, Mar 2, 2012 at 12:44 PM, Randy J. Read 
rj...@cam.ac.ukmailto:rj...@cam.ac.uk wrote:
I'm worried when you say that you use the initial job's output MTZ. Refmac 
replaces F with a detwinned F in the output file so you wouldn't be refining 
against your measured data in the subsequent round.

Best wishes

Randy Read


Randy J. Read

On 2 Mar 2012, at 02:00, wtempel wtem...@gmail.commailto:wtem...@gmail.com 
wrote:

 Dear CCp4ers,
 A good morning to everyone.
 Today, I have a structure that I initially refined in space group P6522, 
 1mol/asu.
 Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
 2.61-2.55A: Rsym=39.6%, I/sigma  10
 50.00-6.13: Rsym=6.4%
 Some mild anisotropy in the resolution limits is apparent on the diffraction 
 images. Say, visible spots at 2.2A in one direction, 2.6A in the other.
 Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A 
 resolution, with some difference density for loops that cannot be interpreted 
 with reasonable geometry.
 Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage 
 does not suggest merohedral twinning.
 Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad'd 
 them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my 
 model to a homotetramer and ran Refmac with amplitude based twinning. (Would 
 this be a reasonable input to twin refinement?)
 From the output coordinates:
 REMARK   3  TWIN DETAILS
 REMARK   3   NUMBER OF TWIN DOMAINS  :4
 REMARK   3  TWIN DOMAIN   :1
 REMARK   3  TWIN OPERATOR :  H,  K,  L
 REMARK   3  TWIN FRACTION : 0.269
 REMARK   3  TWIN DOMAIN   :2
 REMARK   3  TWIN OPERATOR : -K, -H, -L
 REMARK   3  TWIN FRACTION : 0.171
 REMARK   3  TWIN DOMAIN   :3
 REMARK   3  TWIN OPERATOR :  K,  H, -L
 REMARK   3  TWIN FRACTION : 0.258
 REMARK   3  TWIN DOMAIN   :4
 REMARK   3  TWIN OPERATOR : -H, -K,  L
 REMARK   3  TWIN FRACTION : 0.302
 Does this establish twinning versus underestimated symmetry? And what do I 
 need to know about my free-R? Did refmac assign a new flag? Whereas the 
 output file's flags are all 1s and 0s, the input file had 0 ... 19. During 
 the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was 
 stuck 30% when I used the initial job's output MTZ.
 Many thanks in advance for your helpful comments.
 Wolfram Tempel




--

ARKA CHAKRABORTY
CAS in Crystallography and Biophysics
University of Madras
Chennai,India


Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] twin refinement in refmac

[arka chakraborty]

Hi all,

Thanks for the express replies. Your insights along with the article by
Prof. Garib pointed to by Prof. Pavel completes the story for me.

Regards,

ARKO

On Fri, Mar 2, 2012 at 3:09 PM, Steiner, Roberto
roberto.stei...@kcl.ac.ukwrote:

 On 2 Mar 2012, at 08:01, arka chakraborty wrote:

 Hi all,

 I will like to know, as a follow up of what Prof. Randy Read said, what
 should be done to do the refinement against the measured data and not the
 detwinned F( which refmac outputs in the mtz after twin refinement), during
 subsequent refinements.


 Operationally, don't put in the MTZ in field of the GUI something that
 Refmac generated for you in a previous run as MTZ out file. Always use as
 MTZ in your original data file.

 And also, I would like to know how to ensure that the free R generated
 takes twinning into account if I am not using phenix.


 Refmac does take in consideration the twin law(s) when handling free
 reflections . This is the case even if you have generated your free
 reflections randomly. Internally Refmac will modify your Free set in such a
 way that twin related reflections are in the same group (free or working)
 -- classes mentioned by Garib

 The good thing about this is that twin-related reflections are handled
 properly during refinement irrespective of your Free-set choice.
 The bad thing (Garib please correct me if I am wrong here) is that you
 might end up depositing a Free set which is not that actually used in
 refinement.

 Best wishes
 Roberto



 Thanks in advance,

 Regards,

 ARKO

 On Fri, Mar 2, 2012 at 12:44 PM, Randy J. Read rj...@cam.ac.uk wrote:

 I'm worried when you say that you use the initial job's output MTZ.
 Refmac replaces F with a detwinned F in the output file so you wouldn't be
 refining against your measured data in the subsequent round.

 Best wishes

 Randy Read

 
 Randy J. Read

 On 2 Mar 2012, at 02:00, wtempel wtem...@gmail.com wrote:

  Dear CCp4ers,
  A good morning to everyone.
  Today, I have a structure that I initially refined in space group
 P6522, 1mol/asu.
  Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
  2.61-2.55A: Rsym=39.6%, I/sigma  10
  50.00-6.13: Rsym=6.4%
  Some mild anisotropy in the resolution limits is apparent on the
 diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in
 the other.
  Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like
 3.5A resolution, with some difference density for loops that cannot be
 interpreted with reasonable geometry.
  Rsym is very similar for data scaled in P3, in all resolution shells.
 Xtriage does not suggest merohedral twinning.
  Nevertheless, I extended my free flags in sftools from P6522 to P32 and
 cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I
 expanded my model to a homotetramer and ran Refmac with amplitude based
 twinning. (Would this be a reasonable input to twin refinement?)
  From the output coordinates:
  REMARK   3  TWIN DETAILS
  REMARK   3   NUMBER OF TWIN DOMAINS  :4
  REMARK   3  TWIN DOMAIN   :1
  REMARK   3  TWIN OPERATOR :  H,  K,  L
  REMARK   3  TWIN FRACTION : 0.269
  REMARK   3  TWIN DOMAIN   :2
  REMARK   3  TWIN OPERATOR : -K, -H, -L
  REMARK   3  TWIN FRACTION : 0.171
  REMARK   3  TWIN DOMAIN   :3
  REMARK   3  TWIN OPERATOR :  K,  H, -L
  REMARK   3  TWIN FRACTION : 0.258
  REMARK   3  TWIN DOMAIN   :4
  REMARK   3  TWIN OPERATOR : -H, -K,  L
  REMARK   3  TWIN FRACTION : 0.302
  Does this establish twinning versus underestimated symmetry? And what
 do I need to know about my free-R? Did refmac assign a new flag? Whereas
 the output file's flags are all 1s and 0s, the input file had 0 ... 19.
 During the first run, Rfree dropped to 28%. But on a subsequent run, Rfree
 was stuck 30% when I used the initial job's output MTZ.
  Many thanks in advance for your helpful comments.
  Wolfram Tempel
 




 --

 *ARKA CHAKRABORTY*
 *CAS in Crystallography and Biophysics*
 *University of Madras*
 *Chennai,India*


 Roberto Steiner, PhD
 Group Leader
 Randall Division of Cell and Molecular Biophysics
 King's College London

 Room 3.10A
 New Hunt's House
 Guy's Campus
 SE1 1UL, London, UK
 Tel 0044-20-78488216
 Fax 0044-20-78486435
 roberto.stei...@kcl.ac.uk







-- 

*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*

Re: [ccp4bb] twin refinement in refmac

[Pavel Afonine]

Hi Wolfram,

a few points:

- R-factors in twin refinement vs non-twin refinement are not directly
comparable:

G.N. Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261

http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf

- did you make sure free-R flags assigned having twinning in mind (what
phenix.refine always does)? Otherwise you have a risk of having this:

see page 14 here:
http://phenix-online.org/presentations/latest/pavel_validation.pdf

Pavel


On Thu, Mar 1, 2012 at 6:00 PM, wtempel wtem...@gmail.com wrote:

 Dear CCp4ers,
 A good morning to everyone.
 Today, I have a structure that I initially refined in space group P6522,
 1mol/asu.
 Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
 2.61-2.55A: Rsym=39.6%, I/sigma  10
 50.00-6.13: Rsym=6.4%
 Some mild anisotropy in the resolution limits is apparent on the
 diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in
 the other.
 Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like
 3.5A resolution, with some difference density for loops that cannot be
 interpreted with reasonable geometry.
 Rsym is very similar for data scaled in P3, in all resolution shells.
 Xtriage does not suggest merohedral twinning.
 Nevertheless, I extended my free flags in sftools from P6522 to P32 and
 cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I
 expanded my model to a homotetramer and ran Refmac with amplitude based
 twinning. (Would this be a reasonable input to twin refinement?)
 From the output coordinates:
 REMARK   3  TWIN DETAILS
 REMARK   3   NUMBER OF TWIN DOMAINS  :4
 REMARK   3  TWIN DOMAIN   :1
 REMARK   3  TWIN OPERATOR :  H,  K,  L
 REMARK   3  TWIN FRACTION : 0.269
 REMARK   3  TWIN DOMAIN   :2
 REMARK   3  TWIN OPERATOR : -K, -H, -L
 REMARK   3  TWIN FRACTION : 0.171
 REMARK   3  TWIN DOMAIN   :3
 REMARK   3  TWIN OPERATOR :  K,  H, -L
 REMARK   3  TWIN FRACTION : 0.258
 REMARK   3  TWIN DOMAIN   :4
 REMARK   3  TWIN OPERATOR : -H, -K,  L
 REMARK   3  TWIN FRACTION : 0.302
 Does this establish twinning versus underestimated symmetry? And what do I
 need to know about my free-R? Did refmac assign a new flag? Whereas the
 output file's flags are all 1s and 0s, the input file had 0 ... 19. During
 the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was
 stuck 30% when I used the initial job's output MTZ.
 Many thanks in advance for your helpful comments.
 Wolfram Tempel

Re: [ccp4bb] twin refinement in refmac

[Randy J. Read]

I'm worried when you say that you use the initial job's output MTZ. Refmac 
replaces F with a detwinned F in the output file so you wouldn't be refining 
against your measured data in the subsequent round. 

Best wishes

Randy Read


Randy J. Read

On 2 Mar 2012, at 02:00, wtempel wtem...@gmail.com wrote:

 Dear CCp4ers,
 A good morning to everyone.
 Today, I have a structure that I initially refined in space group P6522, 
 1mol/asu.
 Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
 2.61-2.55A: Rsym=39.6%, I/sigma  10
 50.00-6.13: Rsym=6.4%
 Some mild anisotropy in the resolution limits is apparent on the diffraction 
 images. Say, visible spots at 2.2A in one direction, 2.6A in the other.
 Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A 
 resolution, with some difference density for loops that cannot be interpreted 
 with reasonable geometry.
 Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage 
 does not suggest merohedral twinning.
 Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad'd 
 them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my 
 model to a homotetramer and ran Refmac with amplitude based twinning. (Would 
 this be a reasonable input to twin refinement?)
 From the output coordinates:
 REMARK   3  TWIN DETAILS
 REMARK   3   NUMBER OF TWIN DOMAINS  :4
 REMARK   3  TWIN DOMAIN   :1
 REMARK   3  TWIN OPERATOR :  H,  K,  L
 REMARK   3  TWIN FRACTION : 0.269
 REMARK   3  TWIN DOMAIN   :2
 REMARK   3  TWIN OPERATOR : -K, -H, -L
 REMARK   3  TWIN FRACTION : 0.171
 REMARK   3  TWIN DOMAIN   :3
 REMARK   3  TWIN OPERATOR :  K,  H, -L
 REMARK   3  TWIN FRACTION : 0.258
 REMARK   3  TWIN DOMAIN   :4
 REMARK   3  TWIN OPERATOR : -H, -K,  L
 REMARK   3  TWIN FRACTION : 0.302
 Does this establish twinning versus underestimated symmetry? And what do I 
 need to know about my free-R? Did refmac assign a new flag? Whereas the 
 output file's flags are all 1s and 0s, the input file had 0 ... 19. During 
 the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was 
 stuck 30% when I used the initial job's output MTZ.
 Many thanks in advance for your helpful comments.
 Wolfram Tempel
 

Re: [ccp4bb] Twin - Data reduction and refinement in Refmac

[Garib N Murshudov]

As a general rule intensity based refinement gives higher R-factor especially 
when intensities are weak. Truncate smoothes out data and Rfactors become lower 
(it is not necessary that model becomes better)

In your case it may happen that your space group is higher. To check that you 
can do simple refinement and submit your data+model to Zanuda on the server:

www.ysbl.york.ac.uk/YSBLPrograms/index.jsp

It may be able correct your space group and give higer space group if it is the 
case.

What are Rfactors without twin refinement? If Rfactors with and without twin 
refinement are not very different then using twin would not make much sense.

regards
Garib


On 13 Oct 2010, at 16:01, Peter Chan wrote:

 Hello All,
 
 I am a graduate student working on my first merohedrally twinned data set. 
 Like a few, I am a bit intimidated by it. After some trial and error with the 
 help of some online resources and ccp4bb posts, I seem to have solved the 
 structure. However, I am still unsure about some of the steps taken.
 
 Background:
 My dataset was processed to 1.95 A in XDS, the apparent space group is P622 
 (96 A, 96 A, 92 A,  90, 90, 120). Various tests indicate that I have a 
 twinned dataset. The Rsym of the data when processed in a lower symmetry 
 space group (i.e. P6, P321 and P312) suggest that the real space group may be 
 P6 because its Rsym is lower by ~1-2%. The screw axis could not be 
 unambiguously identified from systematic absences. Molecular replacement by 
 Phaser returned a solution in P6(5) with 2 molecules in the asymmetric unit. 
 This was refined in Refmac with the twin option to R  Rfree of 22% and 25%. 
 The twin fractions are 47% and 53%.
 
 My questions and concerns:
 - First and foremost, is there a chance that I may have processed the data in 
 the wrong space group (or wrongly deduced the data in the right space group)?
 
 - Should the diffraction data be merged or unmerged during the twin 
 refinement in Refmac? The current dataset is fully merged (repeated 
 measurements, Friedel pairs  symmetry related reflections). Would there be 
 an improvement in the twin refinement if some of them are kept unmerged?
 
 - Should the twin refinement be performed on the intensities or structure 
 factor amplitudes? I have tried both (using the same set of Rfree flags): 
 With intensities, the R/Rfree are 22%/25% and twin fractions are 47%/53%. 
 With amplitudes, the R/Rfree are 25%/29% and twin fractions are 44.6%/55.4%. 
 The resulting electron density maps are not significantly different, however. 
 I don't understand why the statistics vary so significantly.
 
 - During the model building, the electron density map appears to be 'weak'. 
 Rebuilding some surface loops (by first deleting them, refining the omit 
 structure, and remodeling into the difference map) which initially has some 
 2Fo-Fc density becomes tricky because there is not much density left in the 
 refined omit structure. Was the initial densities purely a result of model 
 bias or is this related to the twinning of the crystal? Could this also be 
 because Refmac outputs a differently weighed 2Fo-Fc map (if I recall 
 correctly) during twin refinement?
 
 I would be very grateful for any help, comments and suggestions.
 
 Best,
 Peter Chan

Re: [ccp4bb] Twin - Data reduction and refinement in Refmac

[Peter Chan]

Hello Garib,

Thank you for the reply  helpful insight.

I ran the refinement of structure factor amplitudes without the TWIN command, 
and obtained much higher R and Rfree (32% and 36%). Also, in the process, I 
found out that I made a mistake earlier in that the amplitudes were refined as 
intensities.

To summarize the R and Rfree of the refinements:

Structure factors, no twin: 32%, 36%
Structure factors, twin:  21.5%,  25.0%
SF, twin, refined as intensities:   25%, 29% -- wrong setting
Intensities, twin:   22.4%,   25.4%

These results fit into the general rule that you mentioned, and I believe I 
will proceed with the twinned refinement of structure factor amplitudes.

As you suggested, I also submitted the data+model to Zanuda on the server (see 
below), and it appears that the real space group is P6(5).

Best,
Peter

   readability test  passed (Refmac_5.5.0070)
   resolution1.947
   spacegroupP 65
   cell  96.530 96.530 91.930 90.00 90.00 120.00

   Step 1.
   R-factors for the starting model.
   Transformation into a supergroup.

   current time:Oct 13 22:21 BST
   expected end of job (rough estimate):Oct 13 22:52 BST

   -
   | Subgroup | Spacegroup | R.m.s.d. |   Refinement in tested group   |
   |  || from the ||
   |   Ref|| starting |  Rigid   | Restrained  |
   |  || model, A |--|-|
   |  ||  |R |R |  R-free  |
   |--||--|--|--|--|
   |4   | P 65   |  0.0005  |--|  0.2005  |  0.2230  |
   |4   | P 65   |  0.0005  |--|--|--|
   ^

   Step 2.
   Refinements in subgroups.
   There are 4 subgroups to test.

   current time:Oct 13 22:32 BST
   expected end of job: Oct 13 23:04 BST

   ^
   |4   | P 65   |  0.0005  |--|--|--|
   -
   |  1   | P 1|  0.0711  |  0.2937  |  0.1949  |  0.2292  |
   |  2   | P 1 21 1   |  0.0631  |  0.3217  |  0.1971  |  0.2305  |
   |  3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
   |  4   | P 65   |  0.0655  |  0.3321  |  0.1976  |  0.2316  |
   -
   |3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
   ^

   Step 3.
   Refinement of the best model.
   Candidate symmetry elements are added one by one.

   current time:Oct 13 22:43 BST
   expected end of job: Oct 13 23:06 BST

   ^
   |3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
   -
   |  1   | P 1|  0.0714  |  0.2949  |  0.1952  |  0.2293  |
   |  2   | P 1 21 1   |  0.0587  |--|  0.1950  |  0.2306  |
   |  4   | P 65   |  0.0596  |--|  0.1961  |  0.2315  |
   | 16   | P 65 2 2   |  1.6311  |--|  0.4261  |  0.4499  |
   -
   |4   | P 65   |  0.0596  |--|  0.1961  |  0.2315  |
   -

   R-factor in the original subgroup is (almost) the best.
   The original spacegroup assignment seems to be correct.

   end of job:  Oct 13 23:02 BST

Date: Wed, 13 Oct 2010 21:51:57 +0100
From: ga...@ysbl.york.ac.uk
Subject: Re: [ccp4bb] Twin - Data reduction and refinement in Refmac
To: CCP4BB@JISCMAIL.AC.UK



As a general rule intensity based refinement gives higher R-factor especially 
when intensities are weak. Truncate smoothes out data and Rfactors become lower 
(it is not necessary that model becomes better)
In your case it may happen that your space group is higher. To check that you 
can do simple refinement and submit your data+model to Zanuda on the server:
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
It may be able correct your space group and give higer space group if it is the 
case.
What are Rfactors without twin refinement? If Rfactors with and without twin 
refinement are not very different then using twin would not make much sense.
regardsGarib

On 13 Oct 2010, at 16:01, Peter Chan wrote:Hello

Re: [ccp4bb] Twin - Data reduction and refinement in Refmac

[Peter Chan]

Hello Fred,

Thank you for the response.

I have made a mistake in the twin refinement settings (see the other email) and 
the best R  Rfree values I obtained were from the twin refinement of structure 
factor amplitudes, which is about 1% less than the twin refinement of 
intensities.

I have not used Bhat's omit maps before. I will give it a shot and see how it 
may improve my model building.

Best,
Peter


 Date: Wed, 13 Oct 2010 17:35:09 +0200
 From: frederic.velli...@ibs.fr
 To: pc...@hotmail.com
 Subject: Re: [ccp4bb] Twin - Data reduction and refinement in Refmac
 
 Peter Chan wrote:
  Hello All,
 
  I am a graduate student working on my first merohedrally twinned data 
  set. Like a few, I am a bit intimidated by it. After some trial and 
  error with the help of some online resources and ccp4bb posts, I seem 
  to have solved the structure. However, I am still unsure about some of 
  the steps taken.
 
  Background:
  My dataset was processed to 1.95 A in XDS, the apparent space group is 
  P622 (96 A, 96 A, 92 A,  90, 90, 120). Various tests indicate that I 
  have a twinned dataset. The Rsym of the data when processed in a lower 
  symmetry space group (i.e. P6, P321 and P312) suggest that the real 
  space group may be P6 because its Rsym is lower by ~1-2%. The screw 
  axis could not be unambiguously identified from systematic absences. 
  Molecular replacement by Phaser returned a solution in P6(5) with 2 
  molecules in the asymmetric unit. This was refined in Refmac with the 
  twin option to R  Rfree of 22% and 25%. The twin fractions are 47% 
  and 53%.
 
 Usually the R and Rfree are slightly higher with twin refinement than 
 with untwinned data; these figures look satisfactory to me.
 
 
  My questions and concerns:
  - First and foremost, is there a chance that I may have processed the 
  data in the wrong space group (or wrongly deduced the data in the 
  right space group)?
 
  - Should the diffraction data be merged or unmerged during the twin 
  refinement in Refmac? The current dataset is fully merged (repeated 
  measurements, Friedel pairs  symmetry related reflections). Would 
  there be an improvement in the twin refinement if some of them are 
  kept unmerged?
 
  - Should the twin refinement be performed on the intensities or 
  structure factor amplitudes? I have tried both (using the same set of 
  Rfree flags): With intensities, the R/Rfree are 22%/25% and twin 
  fractions are 47%/53%. With amplitudes, the R/Rfree are 25%/29% and 
  twin fractions are 44.6%/55.4%. The resulting electron density maps 
  are not significantly different, however. I don't understand why the 
  statistics vary so significantly.
 
 I would use the refinement that gives the lower R / Rfree (no questions 
 asked).
 
 
  - During the model building, the electron density map appears to be 
  'weak'. Rebuilding some surface loops (by first deleting them, 
  refining the omit structure, and remodeling into the difference map) 
  which initially has some 2Fo-Fc density becomes tricky because there 
  is not much density left in the refined omit structure. Was the 
  initial densities purely a result of model bias or is this related to 
  the twinning of the crystal? Could this also be because Refmac outputs 
  a differently weighed 2Fo-Fc map (if I recall correctly) during twin 
  refinement?
 
 Have you tried Bhat's Omit maps as well? Possible to compute using 
 either sfcheck or omit (the latter is not in ccp4bb).
 
 
  I would be very grateful for any help, comments and suggestions.
 
  Best,
  Peter Chan
 
  

Re: [ccp4bb] Twin - Data reduction and refinement in Refmac

[Peter Chan]

I see. Thank you for the reassuring and helpful pointers.

Best,
Peter

Subject: Re: [ccp4bb] Twin - Data reduction and refinement in Refmac
From: ga...@ysbl.york.ac.uk
Date: Wed, 13 Oct 2010 23:55:56 +0100
CC: CCP4BB@JISCMAIL.AC.UK
To: pc...@hotmail.com




It seems that evidence is convincing: twin is present.  All evidences indicate 
that space group is P6(5) and twin is present.
Theoretically that is what you would expect at the end of refinement if twin is 
present: Huge drop in Rfactor and marginal improvement if any in electron 
density. 
RegardsGarib

On 13 Oct 2010, at 23:41, Peter Chan wrote:Hello Garib,

Thank you for the reply  helpful insight.

I ran the refinement of structure factor amplitudes without the TWIN command, 
and obtained much higher R and Rfree (32% and 36%). Also, in the process, I 
found out that I made a mistake earlier in that the amplitudes were refined as 
intensities.

To summarize the R and Rfree of the refinements:

Structure factors, no twin: 32%, 36%
Structure factors, twin:  21.5%,  25.0%
SF, twin, refined as intensities:   25%, 29% -- wrong setting
Intensities, twin:   22.4%,   25.4%

These results fit into the general rule that you mentioned, and I believe I 
will proceed with the twinned refinement of structure factor amplitudes.

As you suggested, I also submitted the data+model to Zanuda on the server (see 
below), and it appears that the real space group is P6(5).

Best,
Peter

   readability test  passed (Refmac_5.5.0070)
   resolution1.947
   spacegroupP 65
   cell  96.530 96.530 91.930 90.00 90.00 120.00

   Step 1.
   R-factors for the starting model.
   Transformation into a supergroup.

   current time:Oct 13 22:21 BST
   expected end of job (rough estimate):Oct 13 22:52 BST

   -
   | Subgroup | Spacegroup | R.m.s.d. |   Refinement in tested group   |
   |  || from the ||
   |   Ref|| starting |  Rigid   | Restrained  |
   |  || model, A |--|-|
   |  ||  |R |R |  R-free  |
   |--||--|--|--|--|
   |4   | P 65   |  0.0005  |--|  0.2005  |  0.2230  |
   |4   | P 65   |  0.0005  |--|--|--|
   ^

   Step 2.
   Refinements in subgroups.
   There are 4 subgroups to test.

   current time:Oct 13 22:32 BST
   expected end of job: Oct 13 23:04 BST

   ^
   |4   | P 65   |  0.0005  |--|--|--|
   -
   |  1   | P 1|  0.0711  |  0.2937  |  0.1949  |  0.2292  |
   |  2   | P 1 21 1   |  0.0631  |  0.3217  |  0.1971  |  0.2305  |
   |  3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
   |  4   | P 65   |  0.0655  |  0.3321  |  0.1976  |  0.2316  |
   -
   |3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
   ^

   Step 3.
   Refinement of the best model.
   Candidate symmetry elements are added one by one.

   current time:Oct 13 22:43 BST
   expected end of job: Oct 13 23:06 BST

   ^
   |3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
   -
   |  1   | P 1|  0.0714  |  0.2949  |  0.1952  |  0.2293  |
   |  2   | P 1 21 1   |  0.0587  |--|  0.1950  |  0.2306  |
   |  4   | P 65   |  0.0596  |--|  0.1961  |  0.2315  |
   | 16   | P 65 2 2   |  1.6311  |--|  0.4261  |  0.4499  |
   -
   |4   | P 65   |  0.0596  |--|  0.1961  |  0.2315  |
   -

   R-factor in the original subgroup is (almost) the best.
   The original spacegroup assignment seems to be correct.

   end of job:  Oct 13 23:02 BST

Date: Wed, 13 Oct 2010 21:51:57 +0100
From: ga...@ysbl.york.ac.uk
Subject: Re: [ccp4bb] Twin - Data reduction and refinement in Refmac
To: CCP4BB@JISCMAIL.AC.UK

As a general rule intensity based refinement gives higher R-factor especially 
when intensities are weak

Re: [ccp4bb] Twin - Data reduction and refinement in Refmac

[Garib N Murshudov]

It seems that evidence is convincing: twin is present.  All evidences indicate 
that space group is P6(5) and twin is present.

Theoretically that is what you would expect at the end of refinement if twin is 
present: Huge drop in Rfactor and marginal improvement if any in electron 
density. 

Regards
Garib


On 13 Oct 2010, at 23:41, Peter Chan wrote:

 Hello Garib,
 
 Thank you for the reply  helpful insight.
 
 I ran the refinement of structure factor amplitudes without the TWIN command, 
 and obtained much higher R and Rfree (32% and 36%). Also, in the process, I 
 found out that I made a mistake earlier in that the amplitudes were refined 
 as intensities.
 
 To summarize the R and Rfree of the refinements:
 
 Structure factors, no twin: 32%, 36%
 Structure factors, twin:  21.5%,  25.0%
 SF, twin, refined as intensities:   25%, 29% -- wrong setting
 Intensities, twin:   22.4%,   25.4%
 
 These results fit into the general rule that you mentioned, and I believe I 
 will proceed with the twinned refinement of structure factor amplitudes.
 
 As you suggested, I also submitted the data+model to Zanuda on the server 
 (see below), and it appears that the real space group is P6(5).
 
 Best,
 Peter
 
readability test  passed (Refmac_5.5.0070)
resolution1.947
spacegroupP 65
cell  96.530 96.530 91.930 90.00 90.00 120.00
 
Step 1.
R-factors for the starting model.
Transformation into a supergroup.
 
current time:Oct 13 22:21 BST
expected end of job (rough estimate):Oct 13 22:52 BST
 
-
| Subgroup | Spacegroup | R.m.s.d. |   Refinement in tested group   |
|  || from the ||
|   Ref|| starting |  Rigid   | Restrained  |
|  || model, A |--|-|
|  ||  |R |R |  R-free  |
|--||--|--|--|--|
|4   | P 65   |  0.0005  |--|  0.2005  |  0.2230  |
|4   | P 65   |  0.0005  |--|--|--|
^
 
Step 2.
Refinements in subgroups.
There are 4 subgroups to test.
 
current time:Oct 13 22:32 BST
expected end of job: Oct 13 23:04 BST
 
^
|4   | P 65   |  0.0005  |--|--|--|
-
|  1   | P 1|  0.0711  |  0.2937  |  0.1949  |  0.2292  |
|  2   | P 1 21 1   |  0.0631  |  0.3217  |  0.1971  |  0.2305  |
|  3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
|  4   | P 65   |  0.0655  |  0.3321  |  0.1976  |  0.2316  |
-
|3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
^
 
Step 3.
Refinement of the best model.
Candidate symmetry elements are added one by one.
 
current time:Oct 13 22:43 BST
expected end of job: Oct 13 23:06 BST
 
^
|3   | P 32   |  0.0629  |  0.3088  |  0.1938  |  0.2290  |
-
|  1   | P 1|  0.0714  |  0.2949  |  0.1952  |  0.2293  |
|  2   | P 1 21 1   |  0.0587  |--|  0.1950  |  0.2306  |
|  4   | P 65   |  0.0596  |--|  0.1961  |  0.2315  |
| 16   | P 65 2 2   |  1.6311  |--|  0.4261  |  0.4499  |
-
|4   | P 65   |  0.0596  |--|  0.1961  |  0.2315  |
-
 
R-factor in the original subgroup is (almost) the best.
The original spacegroup assignment seems to be correct.
 
end of job:  Oct 13 23:02 BST
 
 Date: Wed, 13 Oct 2010 21:51:57 +0100
 From: ga...@ysbl.york.ac.uk
 Subject: Re: [ccp4bb] Twin - Data reduction and refinement in Refmac
 To: CCP4BB@JISCMAIL.AC.UK
 
 As a general rule intensity based refinement gives higher R-factor especially 
 when intensities are weak. Truncate smoothes out data and Rfactors become 
 lower (it is not necessary that model becomes better)
 
 In your case it may happen that your space group

Re: [ccp4bb] Twin questions: is my crystals twinned or not?

[Eleanor Dodson]

There isnt much evidence for twinning that I can see. Moments sensible, 
Ltest sensible for untwinned data, some distortion of the cumulative 
intensity plot but that could be due to integration problems.


Comparing Rfree in P3 is only proper if you have kept the same FreeR set 
as you assigned in P321.


So I think you probably should stay with P321.
Eleanor

 Parthasarathy Sampathkumar wrote:

Dear All,

Back ground:
This is my first experience with a twined dataset. Crystals belong to a
small domain of 132 aa, out of which ~40 residues appears to be disordered
(~30 of those from C-terminal and C-term His6 tag).

Initial space group: P3 with unit cell dimensions: 62.507   62.507   55.117
90.00  90.00 120.00; Resolution 2.35Angs.

Pointless suggested P321 (space group # 150) as possibility. I determined
structure by MR with Phaser (1 molecule in ASU). After several model
building and refinement cycles R and Rfree got stuck at 24.0% and 31.6%
respectively.

Therefore, I considered P3 space group (now Two molecules in the ASU) with a
twin component. I was only able to add handful residues to the model already
refined in P321. My current R and Rfree factors are 21.0% and 29.1%,
respectively for Two molecules refined in P3 space group.

Questions:

1. H-test in cTruncate suggested a twin fraction of 0.43 for the twin
operator -h-k, k, -l. Where as Refmac5 with Amplitude based twin refinement
gave an initial value of 0.508 for the same operator. Why these values are
different between cTruncate and Refmac5 (is this because I asked Refmac5 do
amplitude Twin refinement instead of Intensity based)?

2. I noticed in Refmac5 log file that twin fractions changes for every cycle
of refinement. During my most recent Refmac5 run Initial estimate of 0.508
for -h-k, k, -l operator changed to 0.504 at the end of 20th cycle. The
corresponding values were 0.519 and 0.529, respectively, in a previous
round. Since twin estimates were based on measured Intensities (in turn
amplitudes) why would they change with refinement (am I missing something
here)?

3. When I repeated my final round of Refmac5 WithOut Twin Refinement my R
and R-free factors are 22.9% and 28.6%, respectively, which also appears to
be OK for 2.35 Angs. data (in fact, slightly better R-free). These values
are likely to improve little bit after completing the solvent model. So, is
this crystal really twinned?

I have attached log files of cTruncate and most recent Refmac5 run with Twin
refinement. Apologies for attachments (at least no image files).

Thank you all in advance for educating me.

-Partha

Re: [ccp4bb] Twin questions: is my crystals twinned or not?

[Anastassis Perrakis]

Hi Partha -

A few thoughts:

1. If you attach logs, at least gzip them ...
2. From the fact that Rfree goes down when twinning is switched off, I  
would think there is no twining.
3. The intensity distribution (moment of E, etc) suggest no twining.  
The twining operator you use is the crystallographic two fold, I think.
4. During refinement the relative fraction of twin is a refined  
parameter, to make you model+twining fit the data. The initial twin  
fraction is only an estimate.
5. Did you consider P3121 or P3221 at all? I think its unlikely, but  
easy to check in Phaser as alternative space group.
6. Do these R/Rfree include TLS refinement and waters? if not they are  
quite Ok, given the missing residues
7. I see you only have 430 free reflections. I would argue they are  
too few to get a reliable Rfree and would aim for more, 10% instead of  
5% will give you about 900. Be careful though in not choosing a new  
Rfree for the refinement from now on.


Good luck -

A.


On 8 Jul 2010, at 20:03, Parthasarathy Sampathkumar wrote:


Dear All,

Back ground:
This is my first experience with a twined dataset. Crystals belong  
to a small domain of 132 aa, out of which ~40 residues appears to be  
disordered (~30 of those from C-terminal and C-term His6 tag).


Initial space group: P3 with unit cell dimensions: 62.507   62.507
55.117  90.00  90.00 120.00; Resolution 2.35Angs.


Pointless suggested P321 (space group # 150) as possibility. I  
determined structure by MR with Phaser (1 molecule in ASU). After  
several model building and refinement cycles R and Rfree got stuck  
at 24.0% and 31.6% respectively.


Therefore, I considered P3 space group (now Two molecules in the  
ASU) with a twin component. I was only able to add handful residues  
to the model already refined in P321. My current R and Rfree factors  
are 21.0% and 29.1%, respectively for Two molecules refined in P3  
space group.


Questions:

1. H-test in cTruncate suggested a twin fraction of 0.43 for the  
twin operator -h-k, k, -l. Where as Refmac5 with Amplitude based  
twin refinement gave an initial value of 0.508 for the same  
operator. Why these values are different between cTruncate and  
Refmac5 (is this because I asked Refmac5 do amplitude Twin  
refinement instead of Intensity based)?


2. I noticed in Refmac5 log file that twin fractions changes for  
every cycle of refinement. During my most recent Refmac5 run Initial  
estimate of 0.508 for -h-k, k, -l operator changed to 0.504 at the  
end of 20th cycle. The corresponding values were 0.519 and 0.529,  
respectively, in a previous round. Since twin estimates were based  
on measured Intensities (in turn amplitudes) why would they change  
with refinement (am I missing something here)?


3. When I repeated my final round of Refmac5 WithOut Twin Refinement  
my R and R-free factors are 22.9% and 28.6%, respectively, which  
also appears to be OK for 2.35 Angs. data (in fact, slightly better  
R-free). These values are likely to improve little bit after  
completing the solvent model. So, is this crystal really twinned?


I have attached log files of cTruncate and most recent Refmac5 run  
with Twin refinement. Apologies for attachments (at least no image  
files).


Thank you all in advance for educating me.

-Partha



34_truncate_anl.log40_refmac5.log

Re: [ccp4bb] Twin questions: is my crystals twinned or not?

[Ethan Merritt]

On Thursday 08 July 2010 11:03:30 am Parthasarathy Sampathkumar wrote:
 Dear All,
 
 Back ground:
 This is my first experience with a twined dataset. Crystals belong to a
 small domain of 132 aa, out of which ~40 residues appears to be disordered
 (~30 of those from C-terminal and C-term His6 tag).
 
 Initial space group: P3 with unit cell dimensions: 62.507   62.507   55.117
 90.00  90.00 120.00; Resolution 2.35Angs.
 
 Pointless suggested P321 (space group # 150) as possibility. I determined
 structure by MR with Phaser (1 molecule in ASU). After several model
 building and refinement cycles R and Rfree got stuck at 24.0% and 31.6%
 respectively.

OK.

 Therefore, I considered P3 space group (now Two molecules in the ASU) with a
 twin component. 

But now you veer off track.  P3 + 0.5 twinning fraction is the same
as P321, except that you have doubled the number of refined parameters
by modelling two copies of the protein rather than one.  This is 
probably not what you want to do.

 I was only able to add handful residues to the model already
 refined in P321. My current R and Rfree factors are 21.0% and 29.1%,
 respectively for Two molecules refined in P3 space group.

Turning on twin refinement in refmac is always expected to drop R slightly,
regardless of whether the structure is actually twinned or not.  I'll leave
it to Garib to explain why this is the case :-)  In other words, given that
you doubled the number of parameters and also turned on twin refinement,
a drop in Rfree from .31 to .29 is not impressive.

I don't think that any of the information you present justifies treating the 
structure as being in P3.

Instead you should be considering the possibility that the structure really
is in P321, but there is a twin law that makes it appear partially hexagonal.
See the table of possible twin laws for P3(?)21:
   http://www.ccp4.ac.uk/html/twinning.html

 Questions:
 
 1. H-test in cTruncate suggested a twin fraction of 0.43 for the twin
 operator -h-k, k, -l. 

Was this relative to a P3 indexing, or a P321 indexing?

 Where as Refmac5 with Amplitude based twin refinement
 gave an initial value of 0.508 for the same operator. 

That's strange. A twinning fraction should never be higher than 0.5
But let's get your true twinning law sorted out first before worrying
about whether refmac should report this as 0.508 or 0.492

Ethan


 Why these values are
 different between cTruncate and Refmac5 (is this because I asked Refmac5 do
 amplitude Twin refinement instead of Intensity based)?
 
 2. I noticed in Refmac5 log file that twin fractions changes for every cycle
 of refinement. During my most recent Refmac5 run Initial estimate of 0.508
 for -h-k, k, -l operator changed to 0.504 at the end of 20th cycle. The
 corresponding values were 0.519 and 0.529, respectively, in a previous
 round. Since twin estimates were based on measured Intensities (in turn
 amplitudes) why would they change with refinement (am I missing something
 here)?
 
 3. When I repeated my final round of Refmac5 WithOut Twin Refinement my R
 and R-free factors are 22.9% and 28.6%, respectively, which also appears to
 be OK for 2.35 Angs. data (in fact, slightly better R-free). These values
 are likely to improve little bit after completing the solvent model. So, is
 this crystal really twinned?
 
 I have attached log files of cTruncate and most recent Refmac5 run with Twin
 refinement. Apologies for attachments (at least no image files).
 
 Thank you all in advance for educating me.
 
 -Partha
 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Twin fractions vs. twin domains

[Garib Murshudov]

I guess you are using version 5.5. In that version in the beginning  
the program finds all possible twin operators and assigns twin  
fraction for each of them. Then it tries to filter out smaller twin  
domains and takes only significant domains. I.e. when twin fractions  
are higher than 0.05 by default.


The number of twin domains should be equal to the number of twin  
fractions. Each twin domain has its own twin fraction.


regards
Garib


On 14 Jun 2010, at 14:58, Paul Lindblom wrote:


Hi everybody,

can anybody tell me the difference between twin domain and twin  
fraction. Refmac just told me that my data have 12 twin domains  
((pseudo)merohedral: one time: 0.113 and eleven times 0.081), but  
only 2 twin fractions ( 0.8924  and  0.1076).


best regards,

Paul

Re: [ccp4bb] twin refinement

[Randy Read]

Hi,

You don't say whether you've considered the possibility that the true symmetry 
is higher than P61, e.g. P6122.  If there's higher symmetry consistent with 
your data, then either pointless or xtriage will tell you which space groups to 
consider for test refinements.  Another good test (if you haven't allowed 
NCS-related copies to diverge in the refinement in P61) is the R vs R test, to 
tell whether the apparent twin operator is really a symmetry operator in the 
model.

Note that the R-factors aren't the best indicator, as they tend to drop when 
you assume perfect twinning, even if it doesn't exist.  I think Garib has some 
of his talks on the web, giving some indication of what you can expect.

Regards,

Randy Read

On 3 Mar 2010, at 04:35, subhash C bihani wrote:

 Hi
 
 i am refining a protein strucutre with space group P61. Intesity statistics
 doesnot suggest any twining but refmac and phenix xtriage suggest a twin
 operator  with fraction 0.48. when refined with this twin operator R factors
 come dowm by 3-5% and also map looks much better. but upon closer inspceion it
 seems that maps are heavily biased toward the model in both refmac and phenix 
 (
 I have mutated one lysine to his and it changed the map to cover his). my
 question is why twin refinement maps are biased and what are the ways to
 overcome this.
 
 my second question is how to decide whether to use twin refinement or not. is 
 it
 depends on R factor statistics or we have to check some other parameters.
 
 thanks in advance
 subhash bihani
 scientific officer
 Bhabha Atomic Research Centre
 Trombay-400085
 Mumbai(M.S.)
 India
 Ph. +912594688 (o)
 +919322191020
 subhash bihani
 scientific officer
 Bhabha Atomic Research Centre
 Trombay-400085
 Mumbai(M.S.)
 India
 Ph. +912594688 (o)
 +919322191020
 subhash bihani
 scientific officer
 Bhabha Atomic Research Centre
 Trombay-400085
 Mumbai(M.S.)
 India
 Ph. +912594688 (o)
 +919322191020
 
 
 
 
 
 -

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] Twin refinement not working in CCP4 6.1.1

[Charles Ballard]

Dear All

this and other fixes are on the ccp4 problems pages

http://www.ccp4.ac.uk/problems.php

Charles Ballard

On 2 Mar 2009, at 16:50, Ronnie Berntsson wrote:

I have the same problem when running the latest ccp4 (6.1.1 on os  
x, updated 1 hour ago via fink). Only way I managed to circumvent  
it is to add the TWIN keyword in the command file as well..


Cheers,
Ronnie Berntsson

On Mar 2, 2009, at 16:06, Carr, SB (Stephen) wrote:


Dear CCP4BB,

I have come across a problem when running refmac5 in CCP4 6.1.1  
via the gui.  I have a twinned data set and so want to refine the  
twin fraction of the data. I selected amplitude based twin  
refinement in the gui, but find that the resulting command file  
does not contain the twin keyword and hence twin refinement does  
not occur.  If I manually edit the command file to include the  
twin keyword then refmac calculates twin fractions etc.  Has  
anyone else come across this problem and if so how did you solve it?


best regards,

Steve Carr


Dr Stephen Carr,
Membrane Protein Laboratory,
Diamond Light Source Ltd,
Harwell Science and Innovation Campus,
Chilton,
Didcot,
OX11 0DE

Tel:(44)1235 778896
Email stephen.c...@diamond.ac.uk


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Re: [ccp4bb] Twin refinement not working in CCP4 6.1.1

[Ronnie Berntsson]

I have the same problem when running the latest ccp4 (6.1.1 on os x,  
updated 1 hour ago via fink). Only way I managed to circumvent it is  
to add the TWIN keyword in the command file as well..


Cheers,
Ronnie Berntsson

On Mar 2, 2009, at 16:06, Carr, SB (Stephen) wrote:


Dear CCP4BB,

I have come across a problem when running refmac5 in CCP4 6.1.1 via  
the gui.  I have a twinned data set and so want to refine the twin  
fraction of the data. I selected amplitude based twin refinement in  
the gui, but find that the resulting command file does not contain  
the twin keyword and hence twin refinement does not occur.  If I  
manually edit the command file to include the twin keyword then  
refmac calculates twin fractions etc.  Has anyone else come across  
this problem and if so how did you solve it?


best regards,

Steve Carr


Dr Stephen Carr,
Membrane Protein Laboratory,
Diamond Light Source Ltd,
Harwell Science and Innovation Campus,
Chilton,
Didcot,
OX11 0DE

Tel:(44)1235 778896
Email stephen.c...@diamond.ac.uk


This e-mail and any attachments may contain confidential, copyright  
and or privileged material, and are for the use of the intended  
addressee only. If you are not the intended addressee or an  
authorised recipient of the addressee please notify us of receipt by  
returning the e-mail and do not use, copy, retain, distribute or  
disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the  
individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any  
attachments are free from viruses and we cannot accept liability for  
any damage which you may sustain as a result of software viruses  
which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in  
England and Wales with its registered office at Diamond House,  
Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11  
0DE, United Kingdom




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Re: [ccp4bb] Twin refinement - selecting FreeR Q for Garib..

[Eleanor Dodson]

Is it true that when doing twinned refinement  REFMAC does not use  the 
assigned FreeR set?


 Eleanor


Roberto Steiner wrote:

Hi Sabine,

If your question is: Is it possible to refine twinned structures with 
Refmac?

My answer is: Yes. Very well.

Best wishes,
Roberto

On 20 Feb 2009, at 16:32, Sabine Schneider wrote:


Hi everyone,

I got good data to 2.4A on a protein-ligand complex. I want to solve the
structure by MR using a model with 45% seq. ID and 55% similarity.
Initially the data appeared to be P622 (pointless, selfrotation function
etc). Unit cell: 145 145 65, MW protein is 28kDa
I prepared the MR model with chainsaw, choping of non-conserved residues
at the C gamma and reset the B-factors. Phaser found a solution, but
with negativ LLG.

I than processed the data in P3, P321, P312 and P6 and  run Phaser
searching all possible alternative spacegroups. The best solution is P3
(4mol/asu) followed by P321 (2mol/asu),both with a LLG of above 400. But
when trying to refine the models in Refmac the R/Rfree stays at ~48%.

Looking at the truncate output and phenix xtriage, twinning is suggested
with the merohedral twin law -h, -k, l and a twin fraction of 40.3%
Using twin refine option in Refmac (5.5.0070), the R/Rfree for the P321
solution drops to around 33%, but the difference between R/Rfree is only
1%. For the solution found in P3 the R/Rfree stays at around 47%.

So I assumed that P321 is the better solution. Is the difference in
R/Rfree only 1%, because the free and work reflections are related
through the twin law?

I used phenix  to assign the free reflections putting in the twin
operators. Doing simulated annealing in phenix, I get a rather large
difference in R/Rfree of  ~7%. Well, I guess I need to do some tweaking
of the parameters in phenix (running the latest phenix and cci_apps).
When I than use these free reflections assigned by phenix in Refmac I
still get only 1.5% difference between R and Rfree?

So is it doable in Refmac, or is my best bet phenix? Any advice what is
the best way to proceed is much appreciated!

Sabine


--
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/


---
Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax   +44 (0)20-7848-6435
e-mail roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Twin refinement - selecting FreeR

[Roberto Steiner]

Hi Sabine,

If your question is: Is it possible to refine twinned structures with  
Refmac?

My answer is: Yes. Very well.

Best wishes,
Roberto

On 20 Feb 2009, at 16:32, Sabine Schneider wrote:


Hi everyone,

I got good data to 2.4A on a protein-ligand complex. I want to  
solve the

structure by MR using a model with 45% seq. ID and 55% similarity.
Initially the data appeared to be P622 (pointless, selfrotation  
function

etc). Unit cell: 145 145 65, MW protein is 28kDa
I prepared the MR model with chainsaw, choping of non-conserved  
residues

at the C gamma and reset the B-factors. Phaser found a solution, but
with negativ LLG.

I than processed the data in P3, P321, P312 and P6 and  run Phaser
searching all possible alternative spacegroups. The best solution  
is P3
(4mol/asu) followed by P321 (2mol/asu),both with a LLG of above  
400. But

when trying to refine the models in Refmac the R/Rfree stays at ~48%.

Looking at the truncate output and phenix xtriage, twinning is  
suggested

with the merohedral twin law -h, -k, l and a twin fraction of 40.3%
Using twin refine option in Refmac (5.5.0070), the R/Rfree for the  
P321
solution drops to around 33%, but the difference between R/Rfree is  
only

1%. For the solution found in P3 the R/Rfree stays at around 47%.

So I assumed that P321 is the better solution. Is the difference in
R/Rfree only 1%, because the free and work reflections are related
through the twin law?

I used phenix  to assign the free reflections putting in the twin
operators. Doing simulated annealing in phenix, I get a rather large
difference in R/Rfree of  ~7%. Well, I guess I need to do some  
tweaking

of the parameters in phenix (running the latest phenix and cci_apps).
When I than use these free reflections assigned by phenix in Refmac I
still get only 1.5% difference between R and Rfree?

So is it doable in Refmac, or is my best bet phenix? Any advice  
what is

the best way to proceed is much appreciated!

Sabine


--
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/


---
Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax   +44 (0)20-7848-6435
e-mail roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Twin refinement - selecting FreeR

[Nathaniel Echols]

 I used phenix  to assign the free reflections putting in the twin
 operators. Doing simulated annealing in phenix, I get a rather large
 difference in R/Rfree of  ~7%. Well, I guess I need to do some tweaking of
 the parameters in phenix (running the latest phenix and cci_apps). When I
 than use these free reflections assigned by phenix in Refmac I still get
 only 1.5% difference between R and Rfree?


Are you certain that you're using the same test set for both programs?
 Refmac expects that 0 marks the test set.  Phenix will recognize this and
adjust to use it automatically, but by default it still uses the Xplor/CNS
convention where the test set is marked 1 and everything else is 0.  If you
flagged reflections with Phenix, it's possible that Refmac is using your
test reflections as your working reflections.  (I suspect that you'd see
other problems too if this was the case, but I've made this same mistake
before and I think it resulted in very close Rwork/Rfree.)

-Nat

Re: [ccp4bb] twin axis in p21

[Isupov, Michail]

Dear Hua,

Your problem sounds like a 'false origin' one, where due to the 
pseudotranslation the molecular replacement
choses the wrong origin out of the two possible ones. Your space group is 
probably P212121.
The best approach is to run Andrey Lebedev's program ZANUDA on YSBL server.

http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp


Best wishes

Misha Isupov


From: CCP4 bulletin board [EMAIL PROTECTED] On Behalf Of Yuan, Hua [EMAIL 
PROTECTED]
Sent: 26 November 2008 01:20
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] twin axis in p21

Dear Colleagues,

I'd like to share with you with a twinning puzzle that's been
troubling me for a while.
I have a ~2.2 A data merged in p212121 space group with unit cell:
41.8300  117.4490  134.4840   90.   90.   90.
Translational NCS was detected but structure solution was able to be
obtained by phased molecular replacement as we have a Au derivative
data set. Obtaining experimental phase or MR alone didn't work.

However, with this model and data set, the refinement didn't work
(with R-free ~40% or higher if with more cycles).  Different twinning
tests have been carried out and no sign of twinning.  All possible
p222 space groups have been tried but no luck or even worse.
Considering that translational symmetry and perfect twinning may make
things deceiving, the data was merged into p21 and a twin-refinement
was performed in phenix.refine.  After 3 cycles of rigid-body and
group ADP, a R-free of ~30% was obtained and the output map looks OK.
It looks like we got it.  But then things get interesting when we
tested other two axis as the p21 unique axis.  With all the three
choices plus corresponding twin-refinement, we could get a similar
R-free (30%).  Besides, the three maps all look OK except for one
missing some side chains.

Then the structure was solve in p1 and Xtriage was used with the hope
that one axis would stand out.  However, the RvsR for all three axis
are almost the same.  Did I miss anything here?  Of course, we could
pick up the one axis we like best and get the structure solved ^---^.
However, this puzzle would eat me alive for a very long time.

Best,

Hua

Re: [ccp4bb] twin

[Eleanor Dodson]

Look at http://www.ccp4.ac.uk/dist/html/twinning.html for introduction..

Eleanor

Li Sheng wrote:
 Hi, Dear All,

 How could I know whether a crystal was twin or not from it's
 diffraction data?
 Thanx in advance.




 Sincerely,
 Li
 07-08-2007 

Re: [ccp4bb] twin fraction varies between crystals?

[Ian Tickle]

 
Here's an interesting paper on The Genesis of Twinned Crystals (from
1945! - it's even printed on simulated aged paper and if you look
closely the aging has an unrealistic plane-group pattern!):

http://www.minsocam.org/msa/collectors_corner/arc/twinorig.htm

It's by the eminent crystallographer Martin J. Buerger who was Prof. of
Mineralogy at MIT (http://en.wikipedia.org/wiki/Buergerite) (those of us
old enough will remember his classic textbooks Elementary
Crystallography and the Precession Method in Crystallography:
http://www.amazon.com/s/ref=nb_ss_b/104-3443522-7876740?url=search-alias
%3Dstripbooksfield-keywords=%22martin+j.+buerger%22Go.x=9Go.y=10Go=G
o).

Anyway, the point is that crystals are never grown under identical
conditions even in the same pot - crystallisation by definition is a
dynamic process so that the precise conditions will vary over time and
even from place to place in the pot, because as a crystal grows the
protein or whatever is depleted from solution and so the conditions in
the solution phase inevitably change over time.  Crystallisation is
necessarily a non-equilibrium process from a supersaturated solution (if
it were truly in equilibrium it would take an infinite time for a
crystal to grow!) - and the degree of supersaturation is known to be
correlated with the frequency of occurrence of growth defects such as
twinning.  As the material is depleted from solution the degree of
supersaturation is reduced, so the rate of growth slows down and defects
including twinning become less likely.  Hence one would hypothesise that
the more highly twinned crystals in a pot would be the ones that had
formed first (or at least formed fastest), and in the case of the
variably twinned needle crystal that I mentioned earlier one would
expect that the crystal had grown from the twinned end towards the
non-twinned end - I don't know if anyone has actually looked at this in
detail!

-- Ian


 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of Mark Mayer
 Sent: 17 April 2007 20:39
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: twin fraction varies between crystals?
 
 For cases where people have had merohedral twinning, did the 
 twin fraction vary substantially 
 between individual crystals grown under indentical 
 conditions? I have no prior experience with 
 merohedral twinning, and was surprised to see that the twin 
 fraction varied substantially as detailed 
 below, and that by screening we were able to get untwinned xtals. 
 
 The project started with a weak home data set for which the 
 twin fraction was 0.478, and which 
 scaled in both H3 and H32. We just came back from APS with 
 data sets from another three crystals, 
 for which the ML twin fraction, estimated using 
 phenix.xtriage with scalepack merged intensities as 
 input, varied from 0.335, 0.219 and 0.02. The latter is 
 refining very nicely, in H3 and will not scale in 
 H32. 
 
 Thanks - Mark
 
 

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 
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Re: [ccp4bb] twin fraction varies between crystals?

[Peter Zwart]

Hi Mark,

Estimating twin fractions is best done on the basis of refining it with 
a model. This can be done with phenix.refine or other programs like 
shelx or CNS.


The ML estimate ofd the twin fraction relies on the correctness of the 
sigmas. The 0.02 is actually the lower limit the ML procedure will 
produce, I should fix that/be more clear when reporting the results I guess.


The fact that the twin fractions vary this much is not surprising I 
think. I guess this depends on the type of twinning (contact vs 
penetration), although I am not sure about this.


Peter






Mark Mayer wrote:
For cases where people have had merohedral twinning, did the twin fraction vary substantially 
between individual crystals grown under indentical conditions? I have no prior experience with 
merohedral twinning, and was surprised to see that the twin fraction varied substantially as detailed 
below, and that by screening we were able to get untwinned xtals. 

The project started with a weak home data set for which the twin fraction was 0.478, and which 
scaled in both H3 and H32. We just came back from APS with data sets from another three crystals, 
for which the ML twin fraction, estimated using phenix.xtriage with scalepack merged intensities as 
input, varied from 0.335, 0.219 and 0.02. The latter is refining very nicely, in H3 and will not scale in 
H32. 


Thanks - Mark

Re: [ccp4bb] twin fraction varies between crystals?

[Christopher Colbert]

I experienced the same behavior.  Crystals from the same drop could have 
varying twin fractions.  Screening for twinning can be done with 
remarkably few degrees of data.  Of course, all proteins and all twins 
aren't equal.  So, don't expect to have varying twin fractions all the 
time. 

Happy Refining,

Chris

On Tue, 17 Apr 2007, Mark Mayer wrote:

For cases where people have had merohedral twinning, did the twin fraction 
vary substantially 
between individual crystals grown under indentical conditions? I have no 
prior experience with 
merohedral twinning, and was surprised to see that the twin fraction varied 
substantially as detailed 
below, and that by screening we were able to get untwinned xtals. 

The project started with a weak home data set for which the twin fraction 
was 0.478, and which 
scaled in both H3 and H32. We just came back from APS with data sets from 
another three crystals, 
for which the ML twin fraction, estimated using phenix.xtriage with 
scalepack merged intensities as 
input, varied from 0.335, 0.219 and 0.02. The latter is refining very 
nicely, in H3 and will not scale in 
H32. 

Thanks - Mark


Christopher L. Colbert, Ph.D.
Assistant Instructor  Phone: (214) 645 5944
University of Texas Southwestern Medical Center   FAX:   (214) 645 5945
6001 Forest Park Lane
Dallas, TX 75390

Re: [ccp4bb] twin fraction varies between crystals?

[Manish C Pathak]

I agree with you Mark. Even in my case the twinning fractions
varied substantially among the different crystals grown in same 
drop. Moreover, I feel the fractions may vary at different part of 
the crystal too.  Please correct me if i am wrong.

regards
Manish


Mark Mayer [EMAIL PROTECTED] wrote: For cases where people have had 
merohedral twinning, did the twin fraction vary substantially 
between individual crystals grown under indentical conditions? I have no prior 
experience with 
merohedral twinning, and was surprised to see that the twin fraction varied 
substantially as detailed 
below, and that by screening we were able to get untwinned xtals. 

The project started with a weak home data set for which the twin fraction was 
0.478, and which 
scaled in both H3 and H32. We just came back from APS with data sets from 
another three crystals, 
for which the ML twin fraction, estimated using phenix.xtriage with scalepack 
merged intensities as 
input, varied from 0.335, 0.219 and 0.02. The latter is refining very nicely, 
in H3 and will not scale in 
H32. 

Thanks - Mark


   
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