Dear Patrick,
I could probably set Analysis to not use 'use-external' when there was no
match. I'll check how tricky it would be.
Yours,
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:
> 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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