Hi,
cp.av is the standard bruker pulse sequence for cross polarization 1D
experiments - i.e. solid state (MAS) NMR. So it should be listed as a
simple 13C 1D, in this case.
As far as I can tell there is not a very good standard set of ssnmr
Bruker pulse sequences, so doing that mapping automatically is not
going to be that trivial. I believe most people have their own custom
file names. Aside from that, it is only for these 1Ds that I even use
the Bruker data - otherwise it would be from nmrpipe and thus the
pprog info is lost anyway.
Could you tell Analysis to not select 'external' if it does not
recognize the pulse sequence? Just leaving it blank would be more
appropriate, perhaps? Indeed it would be neat if one could customize/
personalize the experiment mappings, but this would not do much for
nmrpipe data, as I mentioned above.
As an aside - the experiment types for SSNMR experiments are pretty
basic right now anyway, so even if you would try to map it, you'd have
to add various other transfer mechanisms. For homonuclear transfer it
only seems to list Spindiff right now, and for heteronuclear transfer
only CP. So the mapping would be quite involved to get right, if you
really wanted to be complete and completely correct. Probably this is
not the highest priority since the transfer mechanism is not really
'used' for anything anyway.
One idea: would it be possible to subdivide the sequences into
solution and solid state, and have some sort of button to switch
between them? I realize that the separation is not complete, so I
would not completely want to limit the choice to one or the other.
Patrick
On Oct 2, 2009, at 12:08 PM, Rasmus Fogh wrote:
> Dear Patrick,
>
> The change is only there for Bruker experiments. It now reads the
> pulse program file name, from the $PULPROG line in the acqus file,
> parses it, and compares it with a mapping for standard type Bruker
> pulse program names. When the name is in the mapping it just gives
> you the right ExpPrototype (sometimes a couple of possibilities).
> Much simpler. When there is no match it shows the window you are
> getting.
>
> When that happens, you should set the Category to whatever the
> correct calue is ('through-bond', through-space', 'other' ...) and
> take it from there as you did previously. Pretty much as you were
> doing.
>
> Another question is where the 'cp.av' pulse program name came from.
> Is it the correct name of the pulse progam file? Is this a home-made
> sequence, with a non-Bruker-standard name? What version is the
> Bruker file? Is that indeed what it says in the $PULPROG line? What
> experiment should it be?
>
> If this will be a regular occurrence we have provided for a user-
> specific pulse program name mapping, so that you can enter your own
> local pulse program names. It would have to be made functional, and
> it will not be that easy to use, so we are waiting till we get
> requests before we consider implementing it.
>
> Hope this helps,
>
> Rasmus
>
> ---------------------------------------------------------------------------
> 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 Fri, 2 Oct 2009, Patrick van der Wel wrote:
>
>> One more thing I noticed in v2.1. It seems that the experiment type
>> system has been re-worked (improved??). However, it is not entirely
>> clear to me how this should be used. By default it now selects a
>> 'use external' category, which seems to mean that it used the pulse
>> program name. This seems fine to me, but then I get the following
>> popup (see below) regarding the lack of reference experiment types.
>>
>> From experimenting a bit, it seems that I have to select the
>> 'other' category and then pick the traditional ref exp types, as
>> before. Is this right? Why is it defaulting to the external one
>> which does not seem to work? (Or am I doing something wrong?)
>>
>>
>> Patrick
>>
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