Perhaps some history is worthwhile here: As far as I remember
Before experiment prototypes analysis didn't know how to connect as/bs
together so it just autoswitched based on shift, meaning that you could
have the annoying case of Cga linked to Hgb* etc. However, the make
constraints/shift match constraints options from within analysis seemed
(at least for me) to sort out the translation to XPLOR/CNS format OK
(though Tim couldn't remember explicitly sorting it when I asked him!).
Export through formatConverter was a different matter, though that was
probably what most people were likely to do as they didn't have the IUPAC
compliant version of PARALLHDG 5.3 to match the CNS atom names.
Question to Tim - your previous email was clear about what will happen for
cases where protons are assigned, but what are you going to do where no
protons are assigned, still autoswitch as at present? (I have no problem
with that)
Which all reminds me: Question to Mark Williams, Michael Nilges or
Wolfgang Rieping - has official blessing been granted for the IUPACed
version of PARALLHDG 5.3 yet? I notice that even the straight 5.3 version
is still not available as a standalone thing from the Pasteur site. Any
news on CCPN enabled ARIA 2?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0502&L=CCPNMR&P=R1080&I=-3
Brian
On Wed, 1 Feb 2006, Tim Stevens wrote:
> Val Hga*/Cga etc will be linked in the next release. Hopefully
> tomorrow...
>
> The connectivity information comes from the reference experiment types.
>
> T.
>
>> I'm not sure if this is a designed feature, but it caused me a lot of
>> frustration. For non-stereospecific assignments of prochiral Me-groups
>> of Val and Leu residues atom names are Cga, Cgb, Hga*,Hgb* or Cda*,
>> Cdb*, Hda*, Hdb*. My understanding is that Hga* is connected to Cga,
>> Hgb* is connected to Cgb and so on.
>
>
>
> -------------------------------------------------------------------------------
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> ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- -------
> -------------------------------------------------------------------------------
>
--
Dr. Brian O. Smith ---------------------- B Smith at bio gla ac uk
Division of Biochemistry & Molecular Biology,
Institute Biomedical & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 8640
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