Dear All,
If you have an HNcoCA there is no *direct* transfer between N and CA.
The transfer is indirect, in two steps, via the CO. With the current model
there is no 'TransferType' to represent that. The obvious solution is to
not put in an ExpTransfer. Alternatively one could change the model, but
what TransferType should you use for what might be arbitrary multiply
relaued transfers?
Let us see what Tim says,
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 Wed, 10 May 2006, Gary S. Thompson wrote:
> Tim Stevens wrote:
>
> >Please make sure the title of posts to this list matches the contents - I
> >might have missed this query thinking it was a Format Conveter issue...
> >
> >
> >
> Yep sorry that was human error at the end of a long day. I am not quite
> sure what happened but i was certainly looking for a different subject
> line this morning, and almost missed your reply myself
>
> >
> >
> >
> >> I have an experiment which is an hncoca and I have set the
> >>experiment type H [N[co[CA]]]. However it only seems to have one
> >>ExpTransfer between 1H and 13C there is no H N ExpTransfer
> >>
> >>
> >
> >
> >
> sorry there is a typo here should be 1H-15N (see below)
>
> >Hmm. There should not be an ExpTransfer between the 1H and 13C as the
> >transfer to the 13Ca comes from the unmeasured carbonyl. It is possible
> >that the mapping between the ExpDimRefs and the RefExpDimRefs needs
> >looking at when setting the experiment type. This is an odd one because
> >with different isotopes for each axis there should be no ambiguity with
> >setting this mapping (e.g. unlike HCCH).
> >
> >
> >
> >
> >>2. if I change the type of the experiment to an HNCO I get two
> >>ExpTransfers again
> >>
> >>
> >
> >Here there really should be two between 1H & 15N and between 15N & 13C.
> >
> >
>
> yep thats what i expected
>
> >It would be worth checking that both transfers for HNCO are sensible even
> >if there are two in total. If the transfers are between the wrong dims I
> >would suggest that when the spectrum is loaded, the wrong isotope type is
> >coming through/getting set for the dim numbers.
> >
> >
> >
> >
> >>3. if I add a new spectrum and set the type to hncoca again I only get
> >>one ExpTransfer
> >>
> >>
> >
> >When I use my HNcoCA to test I get one transfer between the 1H and 15N as
> >expected, so I'm a bit baffled.
> >
> >
> but there should be one 15N-13C... unless I am not understanding the
> model right
>
> >Check that the isotopes match the dims and then the refExpDims. If there
> >is still no joy maybe you could send the spectrum data or param file.
> >
> >T.
> >
> >
> don't think that is the problem, the problems seems to be with the
> hncoca experiment type as using the hnca experimnet type gives the
> correct ExpTransfers as shown below
>
> here is output for some simple tests at the console so as to nail things
> a bit better
> for experiment in top.project.nmrExperiments:
> for expTransfer in experiment.expTransfers:
> print expTransfer
> for expDimRef in expTransfer.expDimRefs:
> print expDimRef,expDimRef.sf,','
> print '\n'
>
> experiment type set as hncoca
> <ccp.Nmr.ExpTransfer [5, <ccp.Nmr.ExpDimRef [5, 3, 1]>,
> <ccp.Nmr.ExpDimRef [5, 1, 1]>]>
> <ccp.Nmr.ExpDimRef [5, 3, 1]> 75.952003479, <ccp.Nmr.ExpDimRef [5, 1,
> 1]> 749.468994141,
>
> experiment type set as hnca
> <ccp.Nmr.ExpTransfer [5, <ccp.Nmr.ExpDimRef [5, 3, 1]>,
> <ccp.Nmr.ExpDimRef [5, 2, 1]>]>
> <ccp.Nmr.ExpDimRef [5, 3, 1]> 75.952003479,<ccp.Nmr.ExpDimRef [5, 2, 1]>
> 188.464004517
> <ccp.Nmr.ExpTransfer [5, <ccp.Nmr.ExpDimRef [5, 3, 1]>,
> <ccp.Nmr.ExpDimRef [5, 1, 1]>]>
> <ccp.Nmr.ExpDimRef [5, 3, 1]> 75.952003479,<ccp.Nmr.ExpDimRef [5, 1, 1]>
> 749.468994141
>
> nb thought you might like to know,
> the experimments popup is not updating with the new Exp. Type once you
> have finished editing an experiment type with the the edit experiment
> types popup
>
> regards
> gary
>
> --
> -------------------------------------------------------------------
> Dr Gary Thompson
> Astbury Centre for Structural Molecular Biology,
> University of Leeds, Astbury Building,
> Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
> email: [log in to unmask] Fax +44-113-2331407
> -------------------------------------------------------------------
>
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