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
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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 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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