Hi Edward, The protein itself is a monomer/dimer mix, normally it is a monomer; however, the concentrations at which we observe it at (NMR concentrations are around 1mM, the protein forms a dimer (primarily). Using titration experiments we have found what looks to be an interface (using CSP), and have used a docking program to show what the dimer would look like in regards to the dimer interface and what is geometrically/energetically possible. So we aren't looking for proof of a dimer, but my PI had informed me that our S^2 would not be accurate if we used the pdb of the monomer (due to slower tumbling effecting our relaxation data, basically having data for a dimer, and thus the pdb file must also account for the larger size/slower tumbling, basically since the data is for a dimer, the pdb file/structure should also be that of a dimer so they correlate). However, if the S^2 data doesn't get effected too much whether it is a dimer or monomer, then I guess it doesn't matter too much in this case.
Also, could you tell me the exact modification I need to make to my script? This is what it was before structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4') Is this what I should modify it to? structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4',read_mol=0) Sincerely, Sam On Fri, Sep 30, 2016 at 11:45 AM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > On 30 September 2016 at 19:45, Mahdi, Sam <sam.mahdi....@my.csun.edu> > wrote: > > Sorry, I just want to make sure I fully understand this so I can explain > it > > to my PI: > > No problems, this is by far the most complicated aspect in the field of > NMR ;) > > > > 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. > > Load rather than upload, but yes. > > > > 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). > > S2 is not affected by the reference frame. This only matters for > comparing diffusion tensors. Though you will only ever see one > tensor, as that is what is in your NMR sample (if you have a > monomer-dimer mix, then you're in trouble and will see a lot of > artificial Rex and ns motions). > > > > 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). > > Well, your analysis will always return the same diffusion tensor. If > you want these diffusion tensors to all be in the same frame, use the > relax structure.superimpose user function with the method='fit to > first' argument. Then just pick which will be your reference > structure and superimpose. You can superimpose A and B - separately - > onto the monomer frame. > > Let's pick the monomer as the reference frame. Then: > > - If you superimpose "dimer 1, struct A" to the monomer, you > should find the same tensor. > - If you superimpose "dimer 1, struct B" to the monomer, you > should find the same tensor. > - If you superimpose "dimer 2, struct A" to the monomer, you > should find the same tensor. > - If you superimpose "dimer 2, struct B" to the monomer, you > should find the same tensor. > > If the docking program did not optimise the internal monomer > structure, you will get identical results. Otherwise you'll see minor > internal motion changes. If your PI was hoping that you would be able > to tell him that you have a monomer or one of the 2 dimers in your NMR > tube, well then you will need to start to read many, many papers on > diffusion tensor prediction. But know that all prediction methods > underestimate the diffusion tensor (e.g. David Case is working on this > exact problem for MD simulations). In this case, relaxation data is > not the best NMR method for this. It would be better to use RDCs from > a purely steric alignment and to compare that to what PALES prediction > comes up with (though that itself is still a very rough and imperfect > method). > > 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