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CCPNMR  July 2013

CCPNMR July 2013

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Subject:

Re: Format Converter to XPLOR-NIH

From:

Rasmus Fogh <[log in to unmask]>

Reply-To:

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

Date:

Mon, 29 Jul 2013 11:01:48 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

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TEXT/PLAIN (68 lines)

Dear Sylvain,

As it happens, I disagree with you about the ambiguous case. What you know 
for sure is that the NH (for example) is close to *either* of the protons 
- that is enough to give a signal. This limits the NH position to one of 
two spheres centered on either proton. It is true that what is close to 
one is likely close to the other as well, but that should follow naturally 
from covalent geometry. The volume that is close to *both* protons is 
clearly more restricted than the volume that is close to either of them - 
it is the intersection of the spheres, as opposed to the union. If you 
expand to nuclei with a wider separation, the problem is more obvious. 
Tyr/Phe aromatic protons or Leu/Val methyl groups are separated by over 
2A. Forcing your NH (or whatever) to be close to *both* could move it by 
over 2A.

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 Mon, 29 Jul 2013, Sylvain Broussy wrote:

> Dear Rasmus,
>
> Thank you very much for your answer.
> You are probably right for the stereospecific/non-stereospecific case: XPLOR may have a way to handle it by swapping the two atoms. It is more a question about XPLOR than the Format Converter itself, but could someone please confirm the fact, and tell us the method name and if it is included by default in the last version available for download?
>
> However, for the ambiguous case, I think the program should convert to *both* HB2 and HB3 (and not "OR"): the two atoms have very similar environments (they have very similar chemical shifts), and it is difficult to believe that one of them is close to the NH when the other one is not? This is how I understand the description of the ambiguous case in the "atom browser" section of the online documentation at:
> http://www2.ccpn.ac.uk/documentation/analysis/popups/BrowseAtomsPopup.html
> but I may have missed something?
>
> Sylvain
>
>
>> Dear Sylvain,
>
> Wim Vranken will have to give the final answer, but meanwhile I can maybe
> help a bit:
>
> For the ambiguous case (HB2 and HB3 have the same shift) I think the
> treatment is correct. If you see a peak, that generally means that your HN
> is close to *one* of the HB, but you do not know which (how could you -
> they have the same shift). Converting to HB* would seem to be OK. What do
> you think the program should do here?
>
> For the stereospecific and non-stereospecific case there is the problem
> that XPLOR does not have different atom names for two cases, as far as I
> know. Some programs use stereospecific atom names and then swops the
> chirality around during structure determination. I admit that I do not
> know how XPLOR distinguishes between stereospecific and
> non-stereospecific, but for what it is worth I suspect that you would have
> atom names HB2 and HB3 in eitehr case.
>
> That is all from me. Over to Wim,
>
> 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 Mon, 15 Jul 2013, Sylvain wrote:
>

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