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?


On Fri, Sep 30, 2016 at 2:00 PM, Mahdi, Sam <sam.mahdi....@my.csun.edu>

> 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)

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