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CCPNMR  March 2011

CCPNMR March 2011

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Subject:

Re: N-term capping with PyroGlu

From:

Rasmus Fogh <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Fri, 18 Mar 2011 15:16:28 +0000

Content-Type:

MULTIPART/MIXED

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (116 lines)

Dear Henry,

Yes, I get it now. Basically the ChemComp has some errors and always had. 
The amide proton is not present in any of the variants, as it happens, the 
nitrogen is divalent, and there is some stuff for a non-existent link as 
well.

In the short term we shall look at providing you with a patched version, 
but it might take a few days. Expect a mail next week.

Many of the less commonly used ChemComps have one problem or another. This 
has to do with the fact that they are generated automatically by scripts 
from data in the PDB, that we are adding things not in the PDB, and that 
there are many thousand, too many to check by hand. We are on to this 
problem. Tim has written a ChemComp editor (ChemBuild) now just about in 
alpha test; once that cna be released people would be able to make their 
own variants. We are also considering how to distribute a cleaned-up set, 
and what to do about providing one. Even at best it will be a very long 
time (if ever) before we can clean up all we have (7000+, remember), but 
eventually we will be doing something.

Yours,

Rasmus

---------------------------------------------------------------------------
Dr. Rasmus H. Fogh                  Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK.     FAX (01223)766002

On Fri, 18 Mar 2011, Henry Hocking wrote:

> Thanks Rasmus,
> Yes sorry, my wording was incorrect, it is the neutral form I am
> interested in. In the neutral form the nitrogen of the lactam ring should
> have a proton (internal amide). However this proton doesn't appear in my
> atom browser, in other words I only have Ha,Hba/b, Hga/b but no H.
> 
> Regards,
> 
> Henry
> 
> On 18 Mar 2011, at 14:32, Rasmus Fogh wrote:
>
>       Dear Henry,
>
>       This one is actually correct, I think. pyroglutamic acid has
>       an internal amide, and the only reactive group is the acid
>       group. When that is involved in a link (as it is, for
>       'start') there is nothing left to protonate or deprotonate.
>
>       Yours,
>
>       Rasmus
>
>       ---------------------------------------------------------------------------
>       Dr. Rasmus H. Fogh                  Email:
>       [log in to unmask]
>       Dept. of Biochemistry, University of Cambridge,
>       80 Tennis Court Road, Cambridge CB2 1GA, UK.     FAX
>       (01223)766002
>
>       On Fri, 18 Mar 2011, Henry Hocking wrote:
>
>             Dear developers,
>
>             I noticed that pyroglutamic acid (Ccp Code Pca)
>             exists only in neutral
>
>             form when it's 'Polymer linking' is 'start'.
>             Shouldn't there be an option
>
>             for 'prot:H1' at this position?
>
>             Kind regards,
>
>             Henry
>
>             --------------------------------------------------------
>
>             Henry Hocking, PhD
>
>             Utrecht University 
>
>             Bijvoet Center for Biomolecular Research
>
>             Padualaan 8
>
>             3584 CH Utrecht, The Netherlands
>
>             Phone: +31-30-2532875
>
>             Fax: +31-30-253 7623
>
>             E-mail: [log in to unmask]
> 
> 
> --------------------------------------------------------
> Henry Hocking, PhD
> 
> Utrecht University 
> Bijvoet Center for Biomolecular Research
> Padualaan 8
> 3584 CH Utrecht, The Netherlands
> 
> Phone: +31-30-2532875
> Fax: +31-30-253 7623
> E-mail: [log in to unmask]
> 
> 
> 
> 
> 
> 
>

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