Dear Christoph,
Proper handling of alternative confrmations has been contemplated for a
long time, but not yet implemented. For now I would indeed recommend
having extra chains for the alternative conformations.
If you want to do structure calculations you might need to be smart about
this. I assume that there are quite a few peaks that are the same for all
the conformations? The fully correct way of dealing with the situation
would be to assign each of those explicitly to
conformation-1-or-conformation-2-or-conformation-3. If most of the peask
were separate that would be the way to do it, but if a lot are shared this
would be painful. The smartest way might be to have four chains, and use
them as conf-1, conf-2, conf-3, and same-for-all-three-confs. Then you can
use some quick little scripts at the end to generate restraints for three
diferent structure generations. We can help you with those when it comes
to it. I note that you would need some special purpose scripts anyway,
since peaks from different conformers are likely to have rather different
intensities and need different calibrations.
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 Mon, 9 May 2011, Christoph Goebl wrote:
> hey analysis team/users,
>
> I have a question concerning the proper way to implement a 2nd and 3rd conformation of a protein.
> I have assigned a protein now, but I can see fractional 2nd and 3rd conformational peaks.
> Now, before assigning the NOESY I would like to properly pick that.
>
> I did not see a function in the molecule setup, where I could define additional conformations for parts of the protein.
> So, how can I do that? Should I add a 2nd and 3rd full chain in order to assign a few residues?
> (Basically I planed to do structure calculation with each conformation since the NOEs for different conformations
> seem to vary quite a bit.)
>
> Thanks a lot for your help....
> I just want to do everything properly for the further analysis before I switch to the NOESY...
>
>
> greetz
> Christoph
>
|