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.
|