[ccp4bb] Refmac in i2

[Jonathan Cooper]

In the output statistics part of the GUI there is table of mean B-factors, e.g.
Chain mean B (No. atoms) AAA 23.6( 2596 )AaA 35.4( 29 )AbA 35.2( 10 )AcA 18.9( 
10 )AdA 58.5( 10 )AeA 39.5( 119 )BBB 25.5( 2545 )BaB 42.0( 10 )BbB 46.9( 5 )BcB 
37.3( 92 )
There is an A- and a B-chain in the structure, each with their own waters, but 
can someone explain the AaA, AbA,...AeA, BaB...BcB  notation please, since it 
is not obvious how this relates to the contents of the PDB file. Thank you.




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[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

[Nigel Moriarty]

Folks

Calling for articles and short communications of interest to
structural biologists. The deadline for submission for the July 2019
issue is 20 May 2019.

The previous issue is available http://phenix-online.org/newsletter/

and contains the following.

January 2019 

Short Communications
- MARCO: The Machine Recognition of Crystallization Outcomes

- Building a model the way you do: Map-to-model version 2


Fitting tips #16 – Asn and Gln are remarkably different


FAQ - Are the defaults the best for refinements?


The Computational Crystallography Newsletter (CCN) is an electronic
newsletter for structural biologists, and is published online every 6
months. Feature articles, meeting announcements and reports can be
submitted to me at any time for consideration. Submission of text by
email or word-processing files using the CCN templates is requested.
Past newsletters and a Microsoft Word template are available at
www.phenix-online.org/newsletter
.

Cheers

Nigel
Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov



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Re: [ccp4bb] Linking non-natural nucleotide with other natural nucleotides

[Eleanor Dodson]

Yes - this area is a mess.
However I got round it to some extent by naming the nucleotide as a
standard one ((in your case C) , then adding the heavy atom, and creating
the LINK records between that C and the additional atom(s).

Probably at deposition the moiety should be renames as 5CM  but that gets
rpound the refinement glitch..

Eleanor



On Thu, 2 May 2019 at 06:13, Abhishek Suman <
2fccd9428006-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear experts,
>
> I am trying to insert a non-natural nucleotide (5CM, methylated cytosine)
> at 6th position in a 13-mer DNA. I have generated the CIF file for 5CM
> using ELBOW (Phenix). I tried replacing the Cytosine with 5CM and linking
> the O3' of -1 nucleotide with P of 5CM and o3' of 5CM with P of +1
> nucleotide in coot using "Make link". This adds a "LINK" line in the pdb
> file. But, upon refinement in Phenix, the LINK information goes off.
>
> Can anyone please help me with the covalent linking of 5CM with -1 and +1
> nucleotides? Also, the saved PDB file doesn't contain the CONECT line for
> the HETATM. I want to know, how can I append the CONECT information in my
> PDB for 5CM?
>
> Thanks in advance
>
> Regards
> Abhishek
>
> 
>
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