Re: Using relax with RNA -- September 28, 2006 - 17:16

It looks like relax will need to be modified to handle 13C relaxation
in nucleic acids.  I'll need to think about how to handle multiple
data sets per residue.  I'm sure there will be an easy way to handle
it.

Once that is done, then handling N and C together will be another
problem that will need to solved.  Currently the atom type is assigned
to the 'run'.  It could be modified to be data set specific.  These
shouldn't be particularly difficult problems though.  I'll attempt to
come up with solutions for both problems.

Edward



On 9/29/06, Alexandar Hansen <viochemist@xxxxxxxxx> wrote:
> Great!  In the short run that will be perfect.  In the long run, what can be
> done to run Carbon and Nitrogen relaxation simultaneously?  Or multiple
> carbon relaxation sites?  For instance:
>
> Adenine:  C8-H8 and C2-H2
>  Guanine:  C8-H8 and N1-H1
> Cytidine:  C5-H5 and C6-H6
> Uracil:  N3-H3, C5-H5, and C6-H6
>
> Alex Hansen
>
>
>
>
> On 9/28/06, Edward d'Auvergne < edward.dauvergne@xxxxxxxxx> wrote:
> > relax is only requires residue numbers.  The residue name can be
> > absolutely anything!  Therefore as long as there is one data set per
> > residue then it should be fine.  If there are two or more data sets
> > per residue, then relax will have problems.  That should be fixable if
> > required though.
> >
> > Edward
> >
> >
> > On 9/29/06, Alexandar Hansen <viochemist@xxxxxxxxx> wrote:
> > > Hello,
> > >
> > > I was curious how to go about making an input file for nitrogen
> relaxation
> > > of nucleic acids.  Is it a simple procedure of making the input file
> like
> > > this:
> > >
> > > <R1.600.out>
> > >
> > > Num  Name    Value    Error
> > >   1       G         2.15      0.22
> > >   2       U         1.39      0.15
> > > etc.
> > >
> > >
> > > Alex Hansen
> > >
> > >
> > >
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> >
>
>
>
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