Hi Rasmus,
Renumbering the molecule as a separate operation from the chain would be
completely acceptable - I (and probably others) would just like to be able
to do it.
Cheers,
Andrew
On 12/14/09 3:38 AM, "Rasmus Fogh" <[log in to unmask]> wrote:
> Dear All,
>
> Wayne is right, renumbering the molecule has to be a separate operation
> from renumbering the chain. Consider the common situation where you have a
> symmetrical dimer, and want to use different numbering for the two chains.
> Not that we would necessarily recommend it, but many like it. You really
> would not want to renumber the molecule automatically when you renumbered
> one of the chains. There are no data model problems, and we shall consider
> how to allow molecule renumbering in the user interface (and when).
>
> 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 Sat, 12 Dec 2009, Wayne Boucher wrote:
>
>> Hello,
>>
>> We should ignore the complication (below) of synchronising the chain and
>> molecule and just allow the molecule start number to change independently. It
>> is on the TBD list.
>>
>> Wayne
>>
>> On Fri, 11 Dec 2009, Wayne Boucher wrote:
>>
>>> Hello,
>>>
>>> There is a slight data model issue here. So there are two concepts, chains
>>> and molecules. A molecule is a description of the chemical composition
>>> (including bonds, etc.). A chain is an instantiation of that and can have
>>> coordinates, etc. There can be multiple chains for a given molecule (which
>>> is why this distinction was introduced, I think). The cases where you
>>> found that the seqCode changed are to do with the chain. The Sequences tab
>>> though is about the molecule. Changing the Chain Fragment seq number
>>> affects the Residues of the Chain but not the MolResidues of the associated
>>> Molecule. Now I guess we could have it also change the seqCode of that
>>> (well, assuming Rasmus doesn't say there is some reason not to). But what
>>> if there are two chains and the seqCode has been changed for one of the
>>> chains but not the other. But I guess if there is only one chain that is
>>> not really an issue.
>>>
>>> Wayne
>>>
>>> On Fri, 11 Dec 2009, Andrew Fowler wrote:
>>>
>>>> I think I may have found a bug, or at least an inconsistency. Analysis
>>>> 2.1.2, Mac OS X 10.4.11 (probably irrelevant), installed from the package
>>>> and updated yesterday.
>>>>
>>>> I recently found out that I've been using a numbering scheme for the
>>>> peptide
>>>> in a complex that's inconsistent with everyone else. So, I decided to
>>>> renumber the peptide (MS1, chain B, protein is chain A and unchanged).
>>>>
>>>> Main: Molecule: Molecules, in the first tab (Chains), click on chain B and
>>>> in the Fragments portion at the bottom changed Start Seq Number from 156
>>>> to
>>>> 400. Analysis "thought" for a little while.
>>>>
>>>> The residue numbers on peak labels updated immediately. They are updated
>>>> correctly in the spin systems panel, resonances panel, atom browser, and
>>>> peak table. However, if I Show Sequence for the peptide, the old numbering
>>>> is still there.
>>>>
>>>> Am I doing this wrong, is this something that can be remedied, or is this
>>>> something inherent in the data model? I did "save as" so I have the
>>>> project
>>>> both before and after.
>>>>
>>>> Cheers,
>>>> Andrew
>>>>
>>>>
>>>> --
>>>> Dr. Andrew Fowler | University of Iowa
>>>> Associate Director | B291 Carver Biomedical Research
>>>> Building
>>>> Medical NMR Facility | Iowa City, IA 52242
>>>> [log in to unmask]
>>>>
>>>
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