Sorry, I just want to make sure I fully understand this so I can explain it to my PI: So if there is symmetry, I can upload the same pdb file with the dimer (set A and B) but tell it to read only one set. Since S^2 isn't effected too much versus a dimer versus a monomer, the only thing that is important is the change in co-ordinates of one set of the dimer (i.e. the differnence in co-ordinates between set A in a monomer, and set A in a dimer co-ordinates, or set A in a different version of that dimer's co-ordinates). I say this because I have already run my protein's data with the pdb structure of the monomer, and I have 2 different pdb files the docking program gave back for the dimer (2 different ways the dimer could form from one interface).
Sincerely, Sam On Fri, Sep 30, 2016 at 10:29 AM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi Sam, > > Please see below: > > > I'm a bit confused to that. If the protein is a dimer, and the tumbling > > decreases, will that not results in altered relaxation data? > > Yes. > > > Won't the > > relaxation data average be higher, since it is relaxing slower due to its > > increased size (tumbler slower in solution=slower relaxation back to > > equilibrium)? > > No. R2 will be higher. R1 could go anywhere. The NOE may not be > affected too much, but it may decrease (maybe). You need to > understand how the diffusion tensor affects the J(w) spectral density > curves to understand how R1 and the NOE will be affected. > > > > Also, doesn't S^2 take into account the overall shape of the > > molecule (as well as tensor type) in it's calculations? > > No. The S2 value is the internal motions of the residue. It is 100% > independent of the global tumbling. > > > > So won't a dimer > > versus a monomer change the results just due to that? > > Not at all. The optimised diffusion tensor should change, and the S2 > value stay the same. > > > > So should I input both, read_mol=0 and read_mol=1? > > No, only one. You can, however, perform a second analysis later with > read_mol=1 (for comparison). > > > > So > > structure.read_pdb(file='cluster1_12.pdb', dir=None, > > read_mol=None, set_mol_name='hRGS4', > > read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None, > verbosity=1, > > merge=False) > > So mol_num=0 will be for chain A and mol_num=1 for chain B? > > This will have the same IndexError as before - relax will not handle > two identical molecules in a model-free analysis at the same time. > Again, this theory simply does not exist. So I haven't added it to > relax. You need to perform the analysis on a single monomer of the > homodimer. But please check for symmetry - if you don't have > symmetry, nobody on the planet can currently analyse non-symmetric > homodimer data. > > 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
