Hello,
On the box size point. Analysis currently does peak finding the Sparky
way, which means finding local extrema subject to certain conditions, and
it does fitting in a not very good way, using parabolas. We certainly
intend to put a different and better peak fitting in (and there ought to
be several options).
Wayne
On Fri, 8 Oct 2004, Brian Smith wrote:
> Marc,
>
> On Fri, 8 Oct 2004, Marc Lenoir wrote:
>
> > I imported a spectrum and I started to assign the crosspeaks. However,
> > I didn't get why the streospecific protons have the numbers 2 and 3 (i.e.
> > HB2 and HB3). Going to CNS latter on, it is not consistent with the name
> > given by CNS (HB2 and HB1 are defined in the topology file of CNS for every
> > amino acid). Also the HN proton (called HN in CNS) is called H in
> > analysis... Is there any reason for this?
>
> This is the IUPAC naming scheme, so it is the way we _should_ be doing
> things. I have modified versions of parallhdg5.3 with this naming
> convention which I have been using for the past few weeks to make sure tha
> they are debugged - I will send them to you.
>
> > -The distances d, dminus and dplus used in the aria-list is also different
> > (i.e , with azara we get 5.0 5.0 0.0 ; with analysis 5.0 0.0 5.0). Clearly,
> > dminus and dplus are swapped. I'm confused because CNS gives the following
> > syntax :
> >
> > assign <atom-selection> <atom-selection> <real> <real> <real>
> > 1st-set 2nd-set distance dminus dplus.
> >
> > But it seems that dminus should be the highest distance (5.0 in my example).
>
> There were some bugs in the code which we have sorted out (off list, I'm
> afraid). Tim has updated the code and a new release is expected
> imminently. (Tim, if it's going to take more than a couple of days let me
> know and I'll post the fixes).
>
> > Finally, a pratical question about how to choose the size of the box when
> > you want to calculate the volume of your crosspeaks?
>
> Peak fitting is done a bit differently in analysis than ANSIG (by
> default), so I'm not sure that the idea of a box size really applies.
> Maybe Tim/Wayne could enlighten. This does have implications for how
> crosspeaks that are either imported from another program or picked
> manually (right mouse -> create -> peak) are handled though, which I think
> we need to discuss.
>
> Brian
>
> --
> Dr. Brian O. Smith ---------------------- B.Smith at bio.gla.ac.uk
> Division of Biochemistry & Molecular Biology,
> Institute Biomedical & Life Sciences,
> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> Tel: 0141 330 5167/6459 Fax: 0141 330 8640
>
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