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
