Dear Vicky, dear all,
The way I did the current name mapping was to take the entire pulse
program library of Wolfgang Bermel and set up parsing and mapping. That
was over a thousand pulse program names, I believe. Seeing that this was
the official Bruker library it made sense to include it. Also the parsing
is smart enough to recognise new variants, on the standard Bermel style of
names.
I do not have any pulse program that includes the letters 'av', nor
anything with 'cp' that looks like iot means 'cross-polarisation'
There are two issues with solid state:
1) Do we have all the ExpPrototypes you people need? Wolfgang had quite a
few that looked solid state specific. If any are missing we definitely
need to add them.
2) Is there a set of pulse program names that is sufficiently official
and/or widespread that it is reasonable to include them in the standard
distribution? If the experiment names generally vary from lab to lab it
might be better to let each lab make its own mapping file. That is not for
the fainthearted, but I could help.
Can anybody give me any information on these two points? Especially BRuker
standard solid state pulse programs, if they exist.
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, Vicky Higman wrote:
>> 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?
>
> I suspect the issue here is that Patrick is doing solid-state NMR. I think
> in general we need to bit of an overhaul and extension of Expt Types for
> solids. The current Expt Types for instance don't include the initial H-C or
> H-N CP step and in reality they probably should. We also need to think about
> what transfer types to use. I think a specific REDOR or TEDOR transfer would
> be good, as this could be linked to distance determinations. The SpinDiff
> transfer type currently covers a multitude of sins - probably no bad thing,
> but the solid-state community ought to decide collectively, what transfer
> types it would be useful to separate out and which ones can just be lumped
> together (e.g. I don't see any real point in distinguishing between PDSD and
> DARR and possibly even PAR, although these technically constitute different
> types of magnetisation transfer).
>
> Would be happy to discuss more of this off-list with anyone interested.
>
> Vicky
>
>
>
>
>
>> 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
>>>
>>
>
> --
> *********************************************************
> Dr. Victoria A. Higman
>
> Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
> NMR-Supported Structural Biology
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> 13125 Berlin
> Germany
> and
> School of Chemistry
> University of Bristol
> Bristol BS8 1TS
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>
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>
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