On 8 August 2016 at 21:04, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote:
> Hi, I had some general questions regarding model-free analysis that came up
> as I was running it. About 2 months ago, I ran model-free on a 126 residue
> protein. The pdb file I used for the protein had an extra 7 residue
> modifier at one of the terminals, which made it 133 residues; thus, my data
> did not match the pdf file. That run took a little over a week, with the
> sphere model running about 2 models, along with every other model being
> about 2. The data for this run I obtained was unusable (values as small as
> 5x10^-30 for S^2). I attributed this to the fact that my pdf files sequence
> did not align with my data.

Do you mean that the residue numbers were out by 7?  I have considered
this, but relax currently has no way of renumbering the residues in a
3D structure or renumbering the residues of the input data.  So
unfortunately you'll either have to use a molecular view to change
your PDF file, or a script or spreadsheet to renumber your input data.

> I adjusted my relax data (simply added 7 residues with no values), and ran
> it again (all settings the same as before, everything automatic).

I don't think that your data will match up to the correct residues.
The residue numbers in the PDB file and the input relaxation data must
be exact matches.

> This time
> it has taken almost a month, with the sphere model on its 20th run. I saw
> in a previous email that the max is 30 iterations. Is it normal to hit the
> max? Does this mean my data is bad if it requires the max 30 iterations?
> Also, why is it running up to 20 now? The 7 residues I added didn't have
> data, so it doesn't run models for them. I assumed there would be a
> difference in time since the data is now attributed to different spins, but
> not this much of a difference.

If the 3D info and input data do not match, then the results for
non-isotropic (ellipsoidal and spheroidal diffusion) will make no
sense.  In relax you should never need to add relaxation data for
these 7 residues, as relax will handle this situation automatically.
What does your input relaxation data look like?



relax (http://www.nmr-relax.com)

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