Hi Stefano,
For the homodimer problem, you will probably have to research that
one. The problem here is that you are measuring different data each
monomer but that this data is averaged via the NMR spectrum. If you
apply the analysis to the full dimer structure, you are essentially
saying that the non-averaged data for each monomer is identical to the
averaged data. If the averaged data should not be used for the
monomer, it would be just as bad using it on the dimer. From memory
there are papers investigating this. And from even more distant
memory, I think I remember someone invoking symmetry arguments -
though I don't remember if this was in a paper, a discussion at a
conference, etc, or even what the conclusions of those symmetry
arguments were. I would be interested to hear if you know more about
this problem and what the solution is. I'm sorry I cannot help with
this relatively rare problem. The key however will be the symmetries
of the ellipsoidal diffusion tensor.
Regards,
Edward
On 10 February 2014 15:56, Stefano Luciano Ciurli
<stefano.ciurli@xxxxxxxx> wrote:
Hi Edward and thanks for your message. Yes, I am looking forward to
mastering your software. I hope I do not bug you with too many questions,
and that the learning curve will be steep.
See below:
Welcome to the relax mailing lists! I have just tried out your PDB
file attached to the bug report. I launched the relax in GUI mode and
performed the following steps:
- Selected a model-free analysis from the new analysis wizard (this is
the special dauvergne_protocol auto-analysis which is worth reading
about to understand what is happening).
- Clicked on the 'Spin editor' button.
- Clicked on the 'Load spins' button in the spin editor window.
- Selected the option 'From a new PDB file' in the spin loading wizard.
- Loaded your PDB file.
- Set the spin ID to '@N' and '@H' to load the 15N and 1H spins of the
backbone. '@NE1' and '@HE1' spins should probably be loaded as well.
- Click on 'Finish'.
I think I did all the steps that you describe here below yesterday, except
fot the only fact that I changed the string about the molecule name, which
seems unlikely to be the cause of my failure.
Now, and I did it several times, I do not have any problems in reading the
spins for the PDB file. OK then!
I can now see the 15N and 1H spins for two molecules. To perform a
model-free analysis, I could simply delete one of the two molecules
and continue.
question arises: the protein is a homodimer in solution, and I do not think
I should delete any spin nor molecule. Am I correct? If I do, I start from
a wrong geometric model, no?
Stefano
Re: [sr #3110] Spins from PDB