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Subject:

Re: few questions

From:

Rasmus Fogh <[log in to unmask]>

Reply-To:

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

Date:

Tue, 6 Oct 2009 18:50:39 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (86 lines)

Dear All,

An additional comment:

Analysis is built so that it (re)calculates shifts from the positions of 
peaks they are assigned to. I once used to control the precise frequencies 
to use carefully one by one, and was sceptical of this averaging business 
at the start, but it does save you a lot of work. Setting the weight of 
all spectra to zero should nullify the averaging.

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 Tue, 6 Oct 2009, Wayne Boucher wrote:

> Hello,
>
> Tim says (interspersed below):
>
>> Date: Tue, 6 Oct 2009 13:49:47 +0100
>> From: Lalit Deshmukh <[log in to unmask]>
>> Reply-To: CcpNmr software mailing list <[log in to unmask]>
>> To: [log in to unmask]
>> Subject: few questions
>> 
>> Hi,
>> 1)I have almost 90% complete chemical shift table (in CYANA format,
>> generated by CARA). I import it to analysis using format converter which
>> does a decent job except for Val and Leu residues. The methyl groups
>> (CD1,CD2,CG1,CG2) are imported non- stereospecifically , thus when I create
>> synthetic peak list, analysis will create the peaks for all combinations
>> (eg: CD1 will be paired with both HD1 and HD2). Is there a way around this 
>> ?
>
> This may be more of a Wim question, but prochirals can be resolved by 
> assigning them stereospecifically if needs be. For non-stereo assigments the 
> covalent links, which would pair the correct H-C, come from assignments in 
> spectra (and knowledge of the 'onebond' dims). If there are no spectrum 
> assignments this cannot be done.
>
>> 2) All my spectra are calibrated for my chemical shift table, however when
>> analysis will create a synthetic peak list, it moves the shifts around.
>> Although there are no  huge differences , I would like to have a fixed
>> chemical shift table ( as in case of PIPP or CARA, both the softwares will
>> not change the shifts unless and until I want to change them). Is there 
>> some
>> way where the shifts will be fixed and synthetic peak list will be 
>> generated
>> based upon that fixed set of resonances?
>
> The synthetic peaks are severely down-weighted so that they have almost no 
> influence on shifts compated to normal peaks. The factor is 0.0001 from 
> memory. They have some influence so that it is still possible to derive 
> shifts from them (e.g. put in a shift list on their own a value is recorded).
>
> I guess the problem comes when you have no real peaks in CCPN, which isn't 
> the case for most people, which would hold the shifts firm. A potential 
> solution is to set Edit Spectrum:Tolerances - Shift Weighting to zero for the 
> spectra that the synthetic shifts are made for.
>
>
>> 3) While generating a synthetic peak list for NOESY spectra, can I specify
>> in advance the threshold for the particular spectrum ( for example in
>> Auremol, the software will calculate the threshold either automatically or
>> manually, and pick the peaks above this threshold)?
>
> Easy enough to add to the to-do list, but hopefully deleting peaks afterward 
> based on intensity should suffice functionally.  [Wayne adds: you can sort on 
> intensity in the peak table by clicking on the header.]
>
>
>> 4) While generating the synthetic peak list (say based on the structure) 
>> lot
>> of peaks are picked multiple times, is there a simple way to remove the
>> duplicate peaks or merge them?
>
> I suspect it will be best to stop the duplication in the first place. I do 
> not have time at the moment though.
>

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