On 30 September 2016 at 17:31, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote: > Hi Gary, > > There is only a monomer version of it on pdb, so if you mean it in that > sense, yes. I obtained results from it; however the S^2 were very high, but > I attributed this to having data for a dimer, but using a monomer pdb file.
Hi Sam, This cannot be the case. The S2 values are often very similar in a monomer and homodimer case. Or a trimer, tetramer, etc. The only difference is that the global tumbling - the diffusion tensor - is slower in the dimer/trimer/tetramer/etc. (and the tensor type and shape will be different due to the different hydrodynamic+water shell shape). > If you mean have I tried to just delete set B from the pdb file I uploaded, > I have not attempted that. With relax, you should never modify the PDB files - relax can do that for you much better and to the PDB standard via the PDB user functions. > So I am a bit confused here, so if I add read_mol=1 instead of my > read_mol=0, it'll only read set A? Sorry, I meant "read_mol=0" for PDB chain ID A. The argument read_mol=1 will pull out chain ID B. > Assuming symmetry, relax will > automatically calculate and determine set B? Assuming symmetry, you will get the identical results for read_mol=0 and read_mol=1. There might be slight differences in bond orientation if the symmetry is not perfect. If there is no symmetry, the relaxation data for monomer A and monomer B will be different, but it will be averaged to a single value. If this is the case, as I said before there is no theory on the planet for properly handling such averaged data, and you cannot perform any model-free, reduced spectral density mapping (J(w) mapping), or other analysis on it. I hope this clarifies the situation a little better. 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
