Hi Edward, So when I ran it as read_mol=0, it gave me the same error. But it worked once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1 was for set B?
Sincerely, Sam On Fri, Sep 30, 2016 at 2:00 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote: > 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