That's interesting to note because the extended tutorial seem to make
the same assumption as I did, it says 0, -1, 0 for sequential
assignment with a preceding C.
On 13 Dec 2005, at 03:57 pm, Wayne Boucher wrote:
> F1 F2 F3 are the dimensions of the spectrum (and hence the peak),
> in the
> order of the data on disk, I think (in theory that might not be
> true but
> in practise I think it is). It is also the order that things are
> listed
> in the Edit Assignment popup. This is independent of window
> dimensions
> and in particular is not in general the same as the x, y, z of the
> windows. So if you have an (H, N, C) spectrum then F1=H, F2=N,
> F3=C but
> this spectrum can get mapped onto a window with x=C, y=H and z=N
> (or any
> of the six permutations). Hope that helps.
>
> Wayne
>
> On Tue, 13 Dec 2005, Murali Vadivelu wrote:
>
>> Eureka!
>>
>> x, y, z != F1 F2 F3 or I have understood it wrong, the way it works
>> in analysis.
>>
>> When, I used F1 0 F2 0 F3 -1, it worked! I have x=1H, y=13C, z=15N,
>> which I thought should be F1, F2, F3, respectively (as mentioned
>> yesterday in the first few e-mails I sent). I discovered this as the
>> N=z changed as I applied the sequential spin system as 0, -1, 0 --
>> after applying the upgrade.
>>
>> On 13 Dec 2005, at 03:05 pm, Murali Vadivelu wrote:
>>
>>> I have upgraded the file. Then restarted analyis, propagated NH
>>> assignment from a 15N-HSQC to an HNCO experiment. I set the atom
>>> type of the CO to C using the 'edit assignment' popup. Then set the
>>> sequential spin system 0, -1, 0. It didn't do anything. I repeated
>>> it many times and no output on the command line either. Nothing
>>> happened. I tried R:Assign:Add to spin system and analysis adds the
>>> CO to the NH spin system and not to a new spin system or an already
>>> existing spin system which corresponds to the C which I created
>>> manually for the CA and CB in CBCACONH spectra.
>>>
>>> To double check, I started anew from a completely different NH in
>>> the 15N-HSQC. I still have the same problem. Sequential spin system
>>> does not seem to work as described. I am pretty sure, by now, I
>>> understand you clearly!
>>>
>>> Could you suggest anything to try out to debug this? I would be
>>> very happy to try out.
>>>
>>>
>>> On 13 Dec 2005, at 11:49 am, Tim Stevens wrote:
>>>
>>>>>>>> Ca, then the same i-1 spin system will be picked up again.
>>>>>> Are there any error messages appearing on the command line where
>>>>>> Analysis
>>>>>> was started?
>>>>>
>>>>> Nope. Not at all... Could it be that analysis is sensitive to
>>>>> which
>>>>> kind of atom is in which axis (C vs N in F3)? Unlikely?
>>>>
>>>> I have just found an error message. It was appearing on the
>>>> command line
>>>> when seq spin system was set for the second time. The bug seems to
>>>> explain
>>>> the issue entirely. A patch has been posted on the update server.
>>>>
>>>> Although I suspect that any error message in your case may be long
>>>> gone,
>>>> i.e. it may not have been triggered after restarting Analysis,
>>>> always look
>>>> out for these as they can save a lot of e-mailing.
>>>>
>>>> Tim
>>>>
>>>> -------------------------------------------------------------------
>>>> --
>>>> ----------
>>>> Dr Tim Stevens Email: [log in to unmask]
>>>> Department of Biochemistry [log in to unmask]
>>>> University of Cambridge Phone: +44 1223 766022 (office)
>>>> 80 Tennis Court Road +44 7816 338275 (mobile)
>>>> Old Addenbrooke's Site +44 1223 364613 (home)
>>>> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
>>>> United Kingdom http://www.pantonia.co.uk
>>>> -------------------------------------------------------------------
>>>> --
>>>> ----------
>>>> ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)
>>>> CO2- -------
>>>> -------------------------------------------------------------------
>>>> --
>>>> ----------
>>
|