Re: [ccp4bb] Lattice-translocation defect (LTD)

[B.Lohkamp]

Hi Daniele,

we had a possibly similar case and in collaboration with Andrey Lebedev 
we demodulated the data using different methods including a novel 
method, DIGS, (see Acta Cryst. (2014). D70, 1680–1694). We have a few 
scripts to analyse the data and to use the described methods. Sadly we 
never got around to make this more user-friendly and/or put into a 
server (probably not even such a high demand?!). Anyway, if you wish we 
can dig out the scripts and try to get the scripts working on your data 
(depending on the disorder).
Would be good to figure out the SG etc before though... Note: pseudo 
precession diffraction pattern (e.g. from labelit) can help in analysis 
of the data.


Cheers,

B

On 11/02/2020 22:31, Daniele de Sanctis wrote:

Hi all,

I'm currently dealing with what I think it is a case of LTD (off-origin 
Patterson peak, with vector along w of ~ 7A and electron density map 
showing a "ghost" map shifted by 7 A). I saw there are quite a few cases 
reported in literature  (for example Hare et al, 2006), but what I could 
not find is how I can demodulate the data. Is there any software that 
can be used for this?


Thank you

Daniele

--
ἀρετή
---
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

[Eleanor Dodson]

I am no expert, but a) a very strong peak 7A from the origin means two
molecules 7A apart?? Most unlikely ..

The first thing to look at is the actual images - Lattice translation
defects usually generate very streaky patterns.
Integration programs can cleverly select a lattice and ignore the
unpredicted pixels - (by the way - why don't the data integration programs
scream when this occurs? )
LTDs usually produce some strange intensity statistics too - what do the
moments/twin tests etc look like?


Otherwise your spacegroup must be wrong, although providing you have got
the right crystalclass, I cant think how that can generate such a Patterson
peak..

Good luck Eleanor
PS - maybe search out another crystal!

On Wed, 12 Feb 2020 at 10:25, Harry Powell - CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi
>
> Something else I should have mentioned - in iMosflm you can sum your
> images for viewing only if you have them as  HDF5 or Pilatus CBF (as well
> as summing them for processing if you have HDF5).
>
> Harry
>
> On 12 Feb 2020, at 10:18, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
> Hi Daniele,
>
> I agree with Wim that the first thing you should check is your space group
> and especially whether a ncs symmetry element has been mistakenly
> identified as being crystallographic. Since your Patterson peak is along w
> (c-axis), you have to change the space group for processing such, that
> there are no rotation axes or other symmetry elements perpendicular to the
> c-axis any more. If you have a low-symmetry space group, you could also
> process in P1 to be absolutely on the safe side. Than you should run MR in
> this lower symmetry space group.
>
> Concerning lattice translocation defects, almost every case is unique and
> I am not aware of any software able to handle this. Here you will have to
> work out the maths for your particular case yourself and apply the
> correction with e.g. sftools. I am a little puzzled by your 7Å vector in
> your (native?) Patterson maps. I guess, if you translate your protein by 7Å
> it will strongly overlap with itself and I guess the same will be true for
> your ghost map. You should also have a look at your diffraction images,
> perhaps after summing them to 1° slices so become human-interpretable. In
> many cases, LTD is associated with a mix of sharp and fuzzy diffraction
> spots. Seeing those would be a strong indicator that you have the problem,
> but there are cases of LTD where all the spots are sharp. You may also want
> to check for statistical disorder.
>
> Good luck!
> Herman
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Wim
> Burmeister
> *Gesendet:* Mittwoch, 12. Februar 2020 08:57
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> Hello,
>
> do you have some details about the space group ? Did the integration not
> miss any sports ? I would rather think of an ncs close to crystallographic
> symmetry, or maybe some twinning problem.
>
> I guess these are Pilatus data, can you combine the frames into 1 degree
> oscillations and try Mosflm processing to see how the patterns integrate ?
>
> Greetings
>
> Wim
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
>
> Hi all,
>
> I'm currently dealing with what I think it is a case of LTD (off-origin
> Patterson peak, with vector along w of ~ 7A and electron density map
> showing a "ghost" map shifted by 7 A). I saw there are quite a few cases
> reported in literature  (for example Hare et al, 2006), but what I could
> not find is how I can demodulate the data. Is there any software that can
> be used for this?
>
> Thank you
>
> Daniele
>
> --
> ἀρετή
> ---
> Daniele de Sanctis, PhD
>
> Structural Biology Group
> ESRF, Grenoble, France
> Tel 33 (0)4 76 88 2869
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc=zf0W1v2hNpjNiCH51uuDnsPp1HJMSGwT3BVyEsh5Q-U=>
>
> --
> Wim Burmeister
>
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website
> <https://url

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

[Harry Powell - CCP4BB]

Hi

Something else I should have mentioned - in iMosflm you can sum your images for 
viewing only if you have them as  HDF5 or Pilatus CBF (as well as summing them 
for processing if you have HDF5).

Harry

> On 12 Feb 2020, at 10:18, Schreuder, Herman /DE  
> wrote:
> 
> Hi Daniele,
>  
> I agree with Wim that the first thing you should check is your space group 
> and especially whether a ncs symmetry element has been mistakenly identified 
> as being crystallographic. Since your Patterson peak is along w (c-axis), you 
> have to change the space group for processing such, that there are no 
> rotation axes or other symmetry elements perpendicular to the c-axis any 
> more. If you have a low-symmetry space group, you could also process in P1 to 
> be absolutely on the safe side. Than you should run MR in this lower symmetry 
> space group.
>  
> Concerning lattice translocation defects, almost every case is unique and I 
> am not aware of any software able to handle this. Here you will have to work 
> out the maths for your particular case yourself and apply the correction with 
> e.g. sftools. I am a little puzzled by your 7Å vector in your (native?) 
> Patterson maps. I guess, if you translate your protein by 7Å it will strongly 
> overlap with itself and I guess the same will be true for your ghost map. You 
> should also have a look at your diffraction images, perhaps after summing 
> them to 1° slices so become human-interpretable. In many cases, LTD is 
> associated with a mix of sharp and fuzzy diffraction spots. Seeing those 
> would be a strong indicator that you have the problem, but there are cases of 
> LTD where all the spots are sharp. You may also want to check for statistical 
> disorder.
>  
> Good luck!
> Herman
>  
> Von: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag von Wim Burmeister
> Gesendet: Mittwoch, 12. Februar 2020 08:57
> An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
> <mailto:owner-ccp...@jiscmail.ac.uk>
>  
> 
> Hello,
> 
> do you have some details about the space group ? Did the integration not miss 
> any sports ? I would rather think of an ncs close to crystallographic 
> symmetry, or maybe some twinning problem.
> 
> I guess these are Pilatus data, can you combine the frames into 1 degree 
> oscillations and try Mosflm processing to see how the patterns integrate ?
> 
> Greetings
> 
> Wim
> 
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
> Hi all,
>  
> I'm currently dealing with what I think it is a case of LTD (off-origin 
> Patterson peak, with vector along w of ~ 7A and electron density map showing 
> a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
> literature  (for example Hare et al, 2006), but what I could not find is how 
> I can demodulate the data. Is there any software that can be used for this?
>  
> Thank you
>  
> Daniele
> 
> -- 
> ἀρετή
> ---
> Daniele de Sanctis, PhD
> 
> Structural Biology Group
> ESRF, Grenoble, France
> Tel 33 (0)4 76 88 2869
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc=zf0W1v2hNpjNiCH51uuDnsPp1HJMSGwT3BVyEsh5Q-U=>
> -- 
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr <mailto:wim.burmeis...@ibs.fr>
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ibs.fr_research_research-2Dgroups_viral-2Dreplication-2Dmachines-2Dgroup-2Dm-2Djamin_team-2D03_article_poxvirus-2Dreplication-2Dmachinery-2Dpresentation_=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc=TVW6imEeLjhMO1RdtSLG3TllkHecM_5maLbcKjHXCz4=>
> map 
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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

[Schreuder, Herman /DE]

Hi Daniele,

I agree with Wim that the first thing you should check is your space group and 
especially whether a ncs symmetry element has been mistakenly identified as 
being crystallographic. Since your Patterson peak is along w (c-axis), you have 
to change the space group for processing such, that there are no rotation axes 
or other symmetry elements perpendicular to the c-axis any more. If you have a 
low-symmetry space group, you could also process in P1 to be absolutely on the 
safe side. Than you should run MR in this lower symmetry space group.

Concerning lattice translocation defects, almost every case is unique and I am 
not aware of any software able to handle this. Here you will have to work out 
the maths for your particular case yourself and apply the correction with e.g. 
sftools. I am a little puzzled by your 7Å vector in your (native?) Patterson 
maps. I guess, if you translate your protein by 7Å it will strongly overlap 
with itself and I guess the same will be true for your ghost map. You should 
also have a look at your diffraction images, perhaps after summing them to 1° 
slices so become human-interpretable. In many cases, LTD is associated with a 
mix of sharp and fuzzy diffraction spots. Seeing those would be a strong 
indicator that you have the problem, but there are cases of LTD where all the 
spots are sharp. You may also want to check for statistical disorder.

Good luck!
Herman

Von: CCP4 bulletin board  Im Auftrag von Wim Burmeister
Gesendet: Mittwoch, 12. Februar 2020 08:57
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>


Hello,

do you have some details about the space group ? Did the integration not miss 
any sports ? I would rather think of an ncs close to crystallographic symmetry, 
or maybe some twinning problem.

I guess these are Pilatus data, can you combine the frames into 1 degree 
oscillations and try Mosflm processing to see how the patterns integrate ?

Greetings

Wim
Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
Hi all,

I'm currently dealing with what I think it is a case of LTD (off-origin 
Patterson peak, with vector along w of ~ 7A and electron density map showing a 
"ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
literature  (for example Hare et al, 2006), but what I could not find is how I 
can demodulate the data. Is there any software that can be used for this?

Thank you

Daniele

--
ἀρετή
---
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869



To unsubscribe from the CCP4BB list, click the following link:
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--
Wim Burmeister

Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr<mailto:wim.burmeis...@ibs.fr>
Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ibs.fr_research_research-2Dgroups_viral-2Dreplication-2Dmachines-2Dgroup-2Dm-2Djamin_team-2D03_article_poxvirus-2Dreplication-2Dmachinery-2Dpresentation_=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc=TVW6imEeLjhMO1RdtSLG3TllkHecM_5maLbcKjHXCz4=>

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Re: [ccp4bb] Lattice-translocation defect (LTD)

[Harry Powell - CCP4BB]

Hi

Apropos Mosflm - if you have HDF5 files from ESRF (or Diamond, probably 
elsewhere) you can sum the images internally to whatever rotation range per 
pseudo image you want (so if you have, say, 0.05º physical images you could 
process 0.1, 0.15, 0.20º, etc), provided you have installed Mosflm 7.3.* (not 
yet distributed as part of CCP4, as far as I can work out [apologies to CCP4 
core group if they’ve done this and I haven’t noticed], although it’s been 
available for quite some time…). 

I wouldn’t recommend summing to 1.0º unless the mosaicity is really quite large 
- iMosflm itself will suggest an appropriate value, and in my limited 
experience of processing reasonable quality datasets (during testing) the 
optimum often turns out to be ~0.2 - 0.5º (based on metrics like CC-1/2, Rmeas, 
I/sig(I) etc).

Just my two ha’porth

Harry

> On 12 Feb 2020, at 07:57, Wim Burmeister  wrote:
> 
> Hello,
> 
> do you have some details about the space group ? Did the integration not miss 
> any sports ? I would rather think of an ncs close to crystallographic 
> symmetry, or maybe some twinning problem. 
> I guess these are Pilatus data, can you combine the frames into 1 degree 
> oscillations and try Mosflm processing to see how the patterns integrate ?
> 
> Greetings
> 
> Wim
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
>> Hi all,
>> 
>> I'm currently dealing with what I think it is a case of LTD (off-origin 
>> Patterson peak, with vector along w of ~ 7A and electron density map showing 
>> a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
>> literature  (for example Hare et al, 2006), but what I could not find is how 
>> I can demodulate the data. Is there any software that can be used for this?
>> 
>> Thank you
>> 
>> Daniele
>> 
>> -- 
>> ἀρετή
>> ---
>> Daniele de Sanctis, PhD
>> 
>> Structural Biology Group
>> ESRF, Grenoble, France
>> Tel 33 (0)4 76 88 2869
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
>> -- 
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr 
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website 
> 
> map 
> 
> 
> Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
> perdu» (Aurélien Barrau) 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Lattice-translocation defect (LTD)

[Wim Burmeister]

  
  
Hello,
do you have some details about the space group ? Did the
  integration not miss any sports ? I would rather think of an ncs
  close to crystallographic symmetry, or maybe some twinning
  problem. 

I guess these are Pilatus data, can you combine the frames into 1
  degree oscillations and try Mosflm processing to see how the
  patterns integrate ?
Greetings
Wim

Le 11/02/2020 à 22:31, Daniele de
  Sanctis a écrit :


  
  
Hi all,


I'm currently dealing with what I think it is a case of LTD
  (off-origin Patterson peak, with vector along w of ~ 7A and
  electron density map showing a "ghost" map shifted by 7 A). I
  saw there are quite a few cases reported in literature  (for
  example Hare et al, 2006), but what I could not find is how I
  can demodulate the data. Is there any software that can be
  used for this?


Thank you


Daniele


-- 
ἀρετή
  ---
  Daniele de Sanctis, PhD
  
  Structural Biology Group
  ESRF, Grenoble, France
  Tel 33 (0)4 76 88 2869
  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  

-- 
  
  
  Wim
Burmeister
  

  

  

  

  

  

   Professeur
  Institut
de Biologie Structurale (IBS) CIBB
  71
avenue des Martyrs / CS 20192
  
   38044 Grenoble Cedex 9,
  FRANCE
  E-mail: wim.burmeis...@ibs.fr
Tel:    +33 (0) 457 42 87 41  
Fax: +33 (0) 476 20 94 00
  website 
                                   
map
  
  
  Changement
climatique : «Les autres combats n’ont
aucun sens si celui-là est perdu» (Aurélien
  Barrau)   
  
  
  

  

  

  

  

  

  

  



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Re: [ccp4bb] Lattice-translocation defect (LTD)

[00000c2488af9525-dmarc-request]

I was wondering why you believe it is a lattice defect rather than NCS. How well does the structure refine and does it have NCS? Do the twinning tests suggest anything?Jon CooperOn 11 Feb 2020 21:31, Daniele de Sanctis  wrote:Hi all,I'm currently dealing with what I think it is a case of LTD (off-origin Patterson peak, with vector along w of ~ 7A and electron density map showing a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in literature  (for example Hare et al, 2006), but what I could not find is how I can demodulate the data. Is there any software that can be used for this?Thank youDaniele-- ἀρετή---Daniele de Sanctis, PhDStructural Biology GroupESRF, Grenoble, FranceTel 33 (0)4 76 88 2869


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[ccp4bb] Lattice-translocation defect (LTD)

[Daniele de Sanctis]

Hi all,

I'm currently dealing with what I think it is a case of LTD (off-origin
Patterson peak, with vector along w of ~ 7A and electron density map
showing a "ghost" map shifted by 7 A). I saw there are quite a few cases
reported in literature  (for example Hare et al, 2006), but what I could
not find is how I can demodulate the data. Is there any software that can
be used for this?

Thank you

Daniele

-- 
ἀρετή
---
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869



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