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CCPNMR  September 2006

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Subject:

Re: Assignment problems

From:

Tim Stevens <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Thu, 14 Sep 2006 13:37:25 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (73 lines)

> I'm trying to assign the same atom to peaks in 2 different spectra (separate
> shift lists), but analysis allows me to do the assignment only in one of
> them. Once I have done that, the atom browser shows that the atom has not
> yet been assigned in the other spectrum/shift list (as expected), but it
> turns out to be impossible to do that. Actually, all atoms that are already
> assigned in shift list 1 seem to be blocked for assignemts in shift list 2
> and the other way round. The shifts in the two experiments are very similar,
> and the experiments are linked to different shift lists anyway, so this is
> not a problem with the tolerances. I recently switched to a newer ccpnmr
> version, I haven't encountered this problem before. Any ideas?


Firstly it is not impossible to make the same atom assignment for peaks
using two different shift lists, Analysis has been built with this sort of
thing very much in mind. Hopefully it is just a question of how to do the
assignment, and on what information it is based. Such assignment, out of
necessity, doesn't work in the same way as assignment within a single
shift list.

The main point is that resonances (linked to atoms or otherwise) which are
assigned to peaks using one shift list will attain chemical shift values
for that shift list only. There is no prior way of knowing what that shift
should be in a different shift list, which by its creation says that the
shift values are different.

For your situation the task of assignment is to choose the same resonances
as in the first shift list and at the same time specify what their shift
value should be. There are several options for assigning peaks to
resonances that only have a shift in a different shift list.

 * Select two equivalent peaks (i.e. they represent the same resonances)
   which use the different peak list and propagate assignments via
   Mouse menu::Assign::Propagate assignments

 * Use the Menu::Crosspeaks::Copy Peak Assignments option to transfer
   large numbers of assignments from one peak list to another related one.

 * If peak positions are within tolerances, make the second experiment use
   the first shift list, assign with the edit assignment popup as normal,
   and then switch the experiment back to the second shift list.

 * Again if the shifts are similar enough, you can 'copy' the shifts into
   the second shift list by moving assigned experiments (i.e. which define
   the shift values) temporarily into the second shift list.

 * If there are anonymous resonances assigned to a peak that uses the
   second shift list, when you try to link these resonances to atoms that
   have representation in the first shift list, Analysis will use the
   existing resonances for those atoms and define a shift in the second
   shift list.


Also, generally but perhaps not in this instance, it is sometimes worth
checking to make sure that shifts have not entered a shift list with an
incorrect value. This can happen if a mistaken assignment is made and
subsequently removed, or if 'cloned' values are not accurate. In such
cases orphaned shifts can be deleted (to be recreated correctly) or have
their values set manually.

Tim

-------------------------------------------------------------------------------
 Dr Tim Stevens			Email: [log in to unmask]
 Department of Biochemistry            [log in to unmask]
 University of Cambridge        Phone: +44 1223 766018 (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- -------
-------------------------------------------------------------------------------

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