Hi Wayne,
I check with L139, V119 and Q344. They appear in the resonance table,
they have a residue assigned to the spin system, but they do not appear
in the chemical shifts table. In total there are 25 residues missing
from the chemical shifts table. Having had a look at the spin systems
table, I discovered that all of these had empty spins systems (i.e.
those with no peaks) associated with an assignment and these were in
fact those that were missing from the chemical shifts table. I deleted
all of those spins systems and the residues then appeared in the
chemical shifts table. I think I've solved the problem but I've
attached the project anyway in case it's of any use to look into.
Kind Regards
Simon
Wayne Boucher wrote:
> Hello,
>
> Tim says that the shifts are still there, they are just not being
> displayed in that particular table, and that is the puzzle. He thinks
> this is because somehow the spin system does not have a residue, even
> though the atoms in the spin system do, although he doesn't know how
> this might have happened (so there's probably a bug lurking
> somewhere). To test this hypothesis out, if you go into the Resonance
> --> Spin Systems dialog, then check whether the relevant spin system
> has a residue assigned, and if not then assign it (Residue button at
> the bottom). If this is not the issue, then can you tar gzip up the
> project (e.g. with Project --> Archive) and send it to us off list.
>
> Wayne
>
> On Wed, 21 Apr 2010, S.P. Skinner wrote:
>
>> Hi Wayne
>>
>> I've just finished checking through all resonances in the Resonance
>> --> Resonances dialog and the Resonance --> Measurement Lists dialog
>> and both match exactly. I've attached screenshots of the peak lists,
>> resonance list and assignment graph showing the discrepancy. Even
>> though P32 and S33 appear in the resonance tables and are marked in
>> the assignment graph, they do not appear in the chemical shift list
>> and there are about 15 similar cases in this project. Strangely, Y30
>> and N31 did not appear in the chemical shift list yesterday, but
>> today they have appeared. Is this some sort of updating on closing
>> the program that's not keeping up?
>>
>> Regards
>>
>> Simon
>>
>> Wayne Boucher wrote:
>>> Hello,
>>>
>>> Tim says to check the following (so this is assuming there is no
>>> stack trace in your Python console indicating an exception has
>>> occurred):
>>>
>>> The Shift List in the Resonance --> Resonances dialog should be the
>>> same as that in the Resonance --> Measurement Lists dialog in the
>>> Measurements Table tab (if that is what you are looking at) and the
>>> same as that in the Chart --> Chemical Shifts Table dialog (if that
>>> is what you are looking at).
>>>
>>> If that doesn't make any sense or it all looks ok then can you send
>>> us screenshots (off list if you want) so that we have a better idea
>>> of the issue.
>>>
>>> Wayne
>>>
>>> On Tue, 20 Apr 2010, S.P. Skinner wrote:
>>>
>>>> Hi guys
>>>>
>>>> I've just finished an assignment and I'm trying to tidy up the
>>>> resonance list and the chemical shift list so any anomalous
>>>> chemical shifts don't appear in the list etc. However, I've
>>>> noticed that 30 of the residues that I have assigned on both the
>>>> assignment graph and in the resonance list, do not appear in the
>>>> chemical shift list at all.
>>>>
>>>> Is this a bug or am I not doing something right?
>>>>
>>>> Cheers
>>>>
>>>> Simon
>>>>
>>>> --
>>>> Simon P Skinner
>>>> Protein Chemistry Group
>>>> Leiden Institute of Chemistry, Universiteit Leiden
>>>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349
>>>> E-mail : [log in to unmask]
>>
>> --
>> Simon P Skinner
>> Protein Chemistry Group
>> Leiden Institute of Chemistry, Universiteit Leiden
>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349
>> E-mail : [log in to unmask]
--
Simon P Skinner
Protein Chemistry Group
Leiden Institute of Chemistry, Universiteit Leiden
Phone: +31 71 527 6089 / Fax: +31 71 527 4349
E-mail : [log in to unmask]
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