Re: [ccp4bb] circular peptide structure refinement

[Joel Tyndall]

You will need to add the "link" line to the PDB file so the software recognises 
the covalent bond.

See the pdb file for 6U6K

Hope this helps

J

From: CCP4 bulletin board  On Behalf Of Jiang Xu
Sent: Thursday, 7 July 2022 10:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] circular peptide structure refinement

Hello everyone,
   I have a peptide that forms a peptide bond between the N terminal and C 
terminal.  I used X-ray crystallography to solve the structure and found the N 
and C terminals are pretty close to each other with extra electron densities 
clearly showing that they form a peptide bond. However in Coot I could not make 
the peptide bond, the two terminals seem to repel each other when I do real 
space refinement in coot and, couldn't form the peptide bond. Any suggestions 
on how to do it?
Thank you,
Best,
Jiang Xu
Lin Chen Research Group
Molecular and Computational Biology
Department of Biological Sciences
University of Southern California



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[ccp4bb] circular peptide structure refinement

[Jiang Xu]

Hello everyone,
   I have a peptide that forms a peptide bond between the N terminal and C
terminal.  I used X-ray crystallography to solve the structure and found
the N and C terminals are pretty close to each other with extra electron
densities clearly showing that they form a peptide bond. However in Coot I
could not make the peptide bond, the two terminals seem to repel each other
when I do real space refinement in coot and, couldn't form the peptide
bond. Any suggestions on how to do it?
Thank you,
Best,
Jiang Xu
Lin Chen Research Group
Molecular and Computational Biology
Department of Biological Sciences
University of Southern California



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[ccp4bb] Postdoctoral position at ICTER in Warsaw, Poland

[Humberto Fernandes]

Dear all

A postdoctoral position in the Integrated Structural Biology lab at The 
International Center for Translational Eye Research (ICTER) in Warsaw, Poland, 
is available for highly motivated biologists, biochemists, or structural 
biologists, funded until the end of 2023. The position involves cloning, 
protein production, purification, characterization, and structural elucidation 
of proteins of the phototransduction pathway.

For details and how to apply, until the 27th of July, see:
https://icter.pl/jobs/junior-postdoctoral-researcher-in-structural-biology/

Feel free to spread this information at your institutes and to interested 
colleagues. And please do not hesitate to contact me if you have any questions.

Thank you, and have a great day,

Humberto



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01-224 Warszawa  email: 
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Re: [ccp4bb] Off topic: Are all storage dewars equal?

[Nukri Sanishvili]

Hi Carmien,
It appears to me that the dewars in your first link are those made by
Taylor Wharton. You can do a search with that name and hopefully find less
expensive options. We've used them for many years and they are good.
Another one, you could try, is VME https://mvebio.com/aluminum-dewars/
We've used them as well and they are good too.

Just make sure to order a dewar with a wide neck/wide mouth so that your
puck holder fits in.
Also, for holding just 7 pucks, you could get away with smaller and less
expensive dewar. However, smaller ones will need adding of LNG more
frequently, so you will have to pick your poison.
Good luck!
Nukri

On Tue, Jul 5, 2022 at 4:13 AM Carmien Tolmie 
wrote:

> Hello everyone,
>
> We want to buy a storage dewar that can house seven unipucks. I have seen
> dewars on the website of the crystallography suppliers (such as the HC35
> https://www.moleculardimensions.com/products/high-capacity-cryogenic-refrigerators),
> which is significantly more expensive than the run-off-the-mill cryogenic
> storage dewars (such as the Biocane73
> https://www.thermofisher.com/order/catalog/product/CK509X5).
>
> Is there something that makes the dewars from the crystallography
> suppliers special? Or can you use any type of cryogenic storage dewar to
> store the pucs?
>
> Thank you very much for your input.
>
> Best wishes,
>
> Carmien
>
>
>
> --
>
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