Re: relax-users Digest, Vol 116, Issue 38

On 29 October 2016 at 23:44, Mahdi, Sam wrote: > Hi Edward, > > I was reading the theory on model free within the manual and I had a quick > question. The d'Auvergne protocol, is that the model-free analysis in > reverse with the universal solution? Yes, that is the

Re: relax-users Digest, Vol 116, Issue 38

On 4 October 2016 at 23:23, Mahdi, Sam wrote: > Hi Edward, > > Just wanted to update you on the status of my runs. I had 2 potential dimer > structures. I ran Chain A and B for one of them, and Chain B for the other. > All the results were all very similar. There was

Re: relax-users Digest, Vol 116, Issue 38

Hi Edward, Just wanted to update you on the status of my runs. I had 2 potential dimer structures. I ran Chain A and B for one of them, and Chain B for the other. All the results were all very similar. There was missing data though throughout (i.e. I had data for some residues for Chain A that

Re: relax-users Digest, Vol 116, Issue 38

On 1 October 2016 at 20:14, Mahdi, Sam wrote: > Hi Edward, > > Oh ok. Thank you for your help, I was able to resolve the problems I had > with both proteins, and now they are both running. Since there is symmetry > within the dimer, both chain A and chain B will give me

Re: relax-users Digest, Vol 116, Issue 38

Hi Edward, Oh ok. Thank you for your help, I was able to resolve the problems I had with both proteins, and now they are both running. Since there is symmetry within the dimer, both chain A and chain B will give me the same S^2 results correct? Sincerely, Sam On Sat, Oct 1, 2016 at 2:21 AM,

Re: relax-users Digest, Vol 116, Issue 38

On 30 September 2016 at 23:42, Mahdi, Sam wrote: > 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? Sorry, I just remembered that the

Re: relax-users Digest, Vol 116, Issue 38

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 wrote: > Hi Edward, > > The protein

Re: relax-users Digest, Vol 116, Issue 38

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

Re: relax-users Digest, Vol 116, Issue 38

On 30 September 2016 at 19:45, Mahdi, Sam 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

Re: relax-users Digest, Vol 116, Issue 38

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

Re: relax-users Digest, Vol 116, Issue 38

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

Re: relax-users Digest, Vol 116, Issue 38

Hi Edward, 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? 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

Re: relax-users Digest, Vol 116, Issue 38

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. If you mean have I tried to just delete set B from the pdb file

Re: relax-users Digest, Vol 116, Issue 38

Hi Sam have you tried with only one set of coordinates (i presume these are both homo dimers with some form of symetry plane or axis? regards gary -- --- Dr Gary Thompson[Leeds Biological NMR Facility] Astbury