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? Regards, Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
