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
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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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