Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

[Navdeep Sidhu]

PS: For a microscopically visible example in proteins, see the lovely
cubic insulin interpenetrating non-merohedral twin crystallized by
Madhumati Sevvana (Fig. 11a; thankfully open-access article):

Madhumati Sevvana, Michael Ruf, Isabel Uson, George M. Sheldrick and
Regine Herbst-Irmer. Non-merohedral twinning: from minerals to proteins.
Acta Cryst. (2019). D75, 1040–1050
.

Best wishes,
Navdeep

---
Dr. Navdeep Singh Sidhu
https://scholar.google.de/citations?user=ZqU1AE0J
---


---
On 17.03.21 11:12, Ana Luísa Moreira de Carvalho wrote:
> Just a short note on this: I often see colleagues using the word
> “twinning" when referring to a crystal that is actually multiple (not
> single).
>
> I think much confusion arises from this. For me, a twin crystal is the
> one that looks single under the microscope and only intensity statistics
> reveal that the diffraction comes from more than one crystal.



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[ccp4bb] Modifications to support for SHEET and ligand SITE records in June 2021

[John Berrisford]

Dear CCP4BB

 

  In
2014, PDBx/mmCIF became the PDB's archive format and the the legacy PDB file
format was frozen. In addition to PDBx/mmCIF files for all entries, wwPDB
produces PDB format-formatted files for entries that can be represented in
this legacy file format (e.g., entries with over 99,999 atoms or with
multi-character chain IDs are only available in PDBx/mmCIF)

As the size and complexity of PDB structures increases, additional
limitations of the legacy PDB format are becoming apparent and need to be
addressed.


Defining complex sheet records


Restrictions in the SHEET record fields in legacy the PDB file format do not
allow for the generation of complex beta sheet topology. Complex beta sheet
topologies include instances where beta strands are part of multiple beta
sheets and other cases where the definition of the strands within a beta
sheet cannot be presented in a linear description. For example, in PDB entry
5wln a large beta barrel structure is created from multiple copies of a
single protein; within the beta sheet forming the barrel are instances of a
single beta strand making contacts on one side with multiple other strands,
even from different chains.

This limitation, however, is not an issue in the PDBx/mmCIF formatted file,
where these complex beta sheet topology can be captured in _struct_sheet,
_struct_sheet_order, _struct_sheet_range, and _struct_sheet_hbond.

Starting June 8th 2021, legacy PDB format files will no longer be generated
for PDB entries where the SHEET topology cannot be generated. For these
structures, wwPDB will continue to provide secondary structure information
with helix and sheet information in the PDBx/mmCIF formatted file.


Deprecation of _struct_site (SITE) records


wwPDB regularly reviews the software used during OneDep biocuration. The
_struct_site and _struct_site_gen categories in PDBx/mmCIF (SITE records in
the legacy PDB file format) are generated by in-house software and based
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Starting in June 2021, the in-house legacy software which produces
_struct_site and _struct_site_gen records will be retired and wwPDB will no
longer generate these categories for newly-deposited PDB entries. Existing
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John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
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[ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

[Jasmine Young]

A new article in /Structure/  
describes new features, including branched representations and 2D SNFG 
images for carbohydrates, identification of ligands of interest, 3D 
views of electron density fit, and 2D images of small molecule geometry.


These enhancements and processes for validation of 3D small-molecular 
structures reflect recommendations from the wwPDB/CCDC/D3R Ligand 
Validation Workshop and the adoption of software through community 
collaborations.


This manuscript also highlights enhancements made since the initial 
implementation of Validation Reports as described in Validation of the 
Structures in the Protein Data Bank (2017) Structure 25: 1916-1927 doi: 
10.1016/j.str.2017.10.009 .


*Enhanced Validation of Small-Molecule Ligands and Carbohydrates in the 
Protein Data Bank *
Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gérard 
Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko 
F. Aoki-Kinoshita, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, 
Stephen K. Burley, and Jasmine Y. Young
(2021) Structure doi: 10.1016/j.str.2021.02.004 



undefined 



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




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Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

[Navdeep Sidhu]

Far as I understand, twins may or may not have macroscopically
recognizable features. Macroscopic (and microscopic) features like
face angles, reaction on etching, polarization of light, etc. can
sometimes indicate twinning for at least a subset of cases, e.g. in
diamond, some forms of quartz, etc. (see Hahn and Klapper, "Twinning of
Crystals" in the International Tables for Crystallography).

Best wishes,
Navdeep

https://scholar.google.de/citations?user=ZqU1AE0J


---
On 17.03.21 11:12, Ana Luísa Moreira de Carvalho wrote:
> Just a short note on this: I often see colleagues using the word
> “twinning" when referring to a crystal that is actually multiple (not
> single).
> 
> I think much confusion arises from this. For me, a twin crystal is the
> one that looks single under the microscope and only intensity statistics
> reveal that the diffraction comes from more than one crystal.
> 
> If a crystal looks multiple, i do not call it a twin. Am i being too
> meticulous on this?
> Thanks!
> 
>> On 16 Mar 2021, at 13:31, Eleanor Dodson
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
>> > wrote:
>>
>> You usually detect twinning most reliably from the intensity
>> statistics - CCP4I2 and Xtriage report those..
>> Eleanor
>>
>> On Tue, 16 Mar 2021 at 07:31, Marina Gárdonyi
>> > > wrote:
>>
>> Dear all,
>>
>> thanks to all who helped me solving the question. You sent me a
>> lot of 
>> comments and information I have not taken into account.
>> After reading all the answers, I have come to the conclusion that
>> the 
>> spots that are very close to each other come from the long cell axis 
>> (57-57-160) and that twinning can probably not be seen in my case. I 
>> should have mentioned that the diffraction images came from an 
>> in-house x-ray machine, recorded with a 0.5 degree rotation range.
>>
>> Thank you all again!
>>
>> Kind regards,
>> Marina
>>
>> -- 
>> Marina Gárdonyi
>>
>> PhD Student, Research Group Professor Dr. Klebe
>>
>> Department of Pharmaceutical Chemistry
>>
>> Philipps-University Marburg
>>
>> Marbacher Weg 6, 35032 Marburg, Germany
>>
>> Phone: +49 6421 28 21392
>>
>> E-Mail: marina@pharmazie.uni-marburg.de
>> 
>>
>> http://www.agklebe.de/ 
>>
>> 
>>
>> 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
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Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

[DUMAS Philippe (IGBMC)]

It seems to me that it is legitimate to refer to what you describe as 
"twinning". That's the difference between merohedral and non-merohedral 
twinning. What you describe is non-merohedral twinning. 
In fact twinning has been (re)discovered by most of the biological community 
after the remarkable article by T.O. Yeates in Methods in Enz. (1997) vol 276A 
pp. 344-358. Only after this reminder did papers in biocrystallography mention 
twinning currently. (I can refer to my own experience because the Yeates' paper 
allowed us (1) to discover the problem of twinning and (2) to solve a twinned 
structure). Probably, your feeling comes from the fact that structural 
biologists were only concerned by solving their structure and never considered 
multiple crystals (non-merohedral twinning) as a real problem, but only as a 
practical problem, since everyone knew that such crystals had to be either let 
aside or broken into single crystals. 
However, twinning has always been extremely well know in mineralogy because it 
is extremely common to see natural crystals showing non-merohedral twinning. 
And mineralogists commonly have long described crystal habits by twinning 
observed with crystals of specific molecules. 

I suggest that you ask google for "macle rutile wurtzite quartz" (macle is 
twinning in French) and you select images. All these photographs are for 
twinned crystals. All of that was extremely well described in a venerable book 
by Friedel in 1911 when none of us was born. 

I think all of that is not just pure semantics. Am I wrong ? 

Philippe Dumas 



De: "Ana Luísa Moreira de Carvalho"  
À: "CCP4BB"  
Envoyé: Mercredi 17 Mars 2021 11:12:53 
Objet: Re: [ccp4bb] Can twinning be seen in the diffraction pattern? 

Just a short note on this: I often see colleagues using the word “twinning" 
when referring to a crystal that is actually multiple (not single). 

I think much confusion arises from this. For me, a twin crystal is the one that 
looks single under the microscope and only intensity statistics reveal that the 
diffraction comes from more than one crystal. 

If a crystal looks multiple, i do not call it a twin. Am i being too meticulous 
on this? 
Thanks! 




On 16 Mar 2021, at 13:31, Eleanor Dodson < [ 
mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk | 
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk ] > wrote: 

You usually detect twinning most reliably from the intensity statistics - 
CCP4I2 and Xtriage report those.. 
Eleanor 

On Tue, 16 Mar 2021 at 07:31, Marina Gárdonyi < [ 
mailto:marina@pharmazie.uni-marburg.de | 
marina@pharmazie.uni-marburg.de ] > wrote: 

BQ_BEGIN
Dear all, 

thanks to all who helped me solving the question. You sent me a lot of 
comments and information I have not taken into account. 
After reading all the answers, I have come to the conclusion that the 
spots that are very close to each other come from the long cell axis 
(57-57-160) and that twinning can probably not be seen in my case. I 
should have mentioned that the diffraction images came from an 
in-house x-ray machine, recorded with a 0.5 degree rotation range. 

Thank you all again! 

Kind regards, 
Marina 

-- 
Marina Gárdonyi 

PhD Student, Research Group Professor Dr. Klebe 

Department of Pharmaceutical Chemistry 

Philipps-University Marburg 

Marbacher Weg 6, 35032 Marburg, Germany 

Phone: +49 6421 28 21392 

E-Mail: [ mailto:marina@pharmazie.uni-marburg.de | 
marina@pharmazie.uni-marburg.de ] 

[ http://www.agklebe.de/ | http://www.agklebe.de/ ] 

 

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[ccp4bb] Postdoctoral position at ICTER in Warsaw, Poland

[Humberto Fernandes]

Dear all 




This is a final reminder for this post. The closing date is 21st March. 



In the Integrated Structural Biology laboratory at The International Center for 
Translational Eye Research (ICTER) in Warsaw, Poland, one postdoctoral position 
is available for a highly motivated biologist, biochemist, or structural 
biologist, for 33 months (maximum planned period of contract: 31/12/2023). The 
position involves cloning, protein production, purification, characterization, 
and structural elucidation of proteins from the visual cycle. 



For details and how to apply until 21st March, see: 

https://ichf.edu.pl/en/job/mcbo-34-2021-mab-2019-12 



Feel free to spread this information at your institutes and to interested 
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To apply, please send the requested documents to icter_j...@ichf.edu.pl with 
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Thank you and have a great day, 



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Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

[Eleanor Dodson]

Yes Ana, I agree although some non-merihedrals where the accident of cell
dimensions mean many spots can overlap but not quite exactly can seem a bit
smeary and "multiple.
Meridral twins do not usually look multiple - they are usually only
revealed by the 2nd moment and other stats..
Eleanor

On Wed, 17 Mar 2021 at 10:13, Ana Luísa Moreira de Carvalho 
wrote:

> Just a short note on this: I often see colleagues using the word
> “twinning" when referring to a crystal that is actually multiple (not
> single).
>
> I think much confusion arises from this. For me, a twin crystal is the one
> that looks single under the microscope and only intensity statistics reveal
> that the diffraction comes from more than one crystal.
>
> If a crystal looks multiple, i do not call it a twin. Am i being too
> meticulous on this?
> Thanks!
>
> On 16 Mar 2021, at 13:31, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> You usually detect twinning most reliably from the intensity statistics -
> CCP4I2 and Xtriage report those..
> Eleanor
>
> On Tue, 16 Mar 2021 at 07:31, Marina Gárdonyi <
> marina@pharmazie.uni-marburg.de> wrote:
>
>> Dear all,
>>
>> thanks to all who helped me solving the question. You sent me a lot of
>> comments and information I have not taken into account.
>> After reading all the answers, I have come to the conclusion that the
>> spots that are very close to each other come from the long cell axis
>> (57-57-160) and that twinning can probably not be seen in my case. I
>> should have mentioned that the diffraction images came from an
>> in-house x-ray machine, recorded with a 0.5 degree rotation range.
>>
>> Thank you all again!
>>
>> Kind regards,
>> Marina
>>
>> --
>> Marina Gárdonyi
>>
>> PhD Student, Research Group Professor Dr. Klebe
>>
>> Department of Pharmaceutical Chemistry
>>
>> Philipps-University Marburg
>>
>> Marbacher Weg 6, 35032 Marburg, Germany
>>
>> Phone: +49 6421 28 21392
>>
>> E-Mail: marina@pharmazie.uni-marburg.de
>>
>> http://www.agklebe.de/
>>
>> 
>>
>> 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
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>>
>
> --
>
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Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

[Ana Luísa Moreira de Carvalho]

Just a short note on this: I often see colleagues using the word “twinning" 
when referring to a crystal that is actually multiple (not single).

I think much confusion arises from this. For me, a twin crystal is the one that 
looks single under the microscope and only intensity statistics reveal that the 
diffraction comes from more than one crystal.

If a crystal looks multiple, i do not call it a twin. Am i being too meticulous 
on this?
Thanks!

> On 16 Mar 2021, at 13:31, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> You usually detect twinning most reliably from the intensity statistics - 
> CCP4I2 and Xtriage report those..
> Eleanor
> 
> On Tue, 16 Mar 2021 at 07:31, Marina Gárdonyi 
>  > wrote:
> Dear all,
> 
> thanks to all who helped me solving the question. You sent me a lot of  
> comments and information I have not taken into account.
> After reading all the answers, I have come to the conclusion that the  
> spots that are very close to each other come from the long cell axis  
> (57-57-160) and that twinning can probably not be seen in my case. I  
> should have mentioned that the diffraction images came from an  
> in-house x-ray machine, recorded with a 0.5 degree rotation range.
> 
> Thank you all again!
> 
> Kind regards,
> Marina
> 
> -- 
> Marina Gárdonyi
> 
> PhD Student, Research Group Professor Dr. Klebe
> 
> Department of Pharmaceutical Chemistry
> 
> Philipps-University Marburg
> 
> Marbacher Weg 6, 35032 Marburg, Germany
> 
> Phone: +49 6421 28 21392
> 
> E-Mail: marina@pharmazie.uni-marburg.de 
> 
> 
> http://www.agklebe.de/ 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
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