Re: Re: -- May 14, 2014 - 17:56

Hi Vineet,

Could you please change your email settings when responding to mailing
list settings?  Your previous message has somehow placed my
nmr-relax.com email address into the footer.  But, more of a worry, it
has also placed my personal Gmail address into the footer!  I have no
idea how that is even possible!!!  This must be avoided, your message
will be archived in 4 different places on the web.  The result will be
a big increase in spam sent to my Gmail account.

Cheers,

Edward


On 14 May 2014 17:48, Panwalkar, Vineet <v.panwalkar@xxxxxxxxxxxxx> wrote:
> Hi Ed,
>
> Thanks for this. I will create the report asap.
>
> Also, as mentioned in the earlier email, in my protein structure, I see a 
> high backbone RMSD for first 5 residues and last 2 residues. When I use 
> just the low energy structure I get one set of diffusion tensor data, which 
> is quite different from what I get then i use the ensemble. I am abit 
> puzzled about why this happens. Is it possible that the change from oblate 
> to ellipsoid, when a 15 structure ensemble is used, might be due to over 
> estimation of the tensor caused by having 15 different structures having 
> highly flexible N and C termini?
>
> Regards,
>
> Vineet
> ________________________________________
> Von: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx]&quot; im 
> Auftrag von &quot;Edward d'Auvergne [edward@xxxxxxxxxxxxx]
> Gesendet: Mittwoch, 14. Mai 2014 17:31
> An: Panwalkar, Vineet
> Cc: relax-users@xxxxxxx
> Betreff: Re:
>
> Dear Vineet,
>
> The problem you are seeing is a simple bug - Dpar is simply being
> displayed twice.  Could you please create a bug report for this?
> Simply fill out the details at
> https://gna.org/bugs/?func=additem&group=relax.  I will then fix the
> problem and the solution will be available with the next relax
> release.  The bug report will be useful for other users
>
> Cheers,
>
> Edward
>
>
> P. S.  I can already see the problem in the relax source code.  See if
> you can see it too in the display() function at
> http://www.nmr-relax.com/api/3.1/pipe_control.diffusion_tensor-pysrc.html#display.
>
>
> On 14 May 2014 17:00, Panwalkar, Vineet <v.panwalkar@xxxxxxxxxxxxx> wrote:
> > Dear users,
> >
> > I have recently carried out two seperate model-free analysis on a ~5 kDa 
> > protein with relaxation data measured at 600, 800 and 900 MHz. I used the 
> > fully automated analysis scripts for the analysis.
> >
> > In the first run, I used the lowest energy structure from my 15 structure 
> > ensemble. I get an oblate diffusion tensor. When I read the results and 
> > ask for diffusion_tensor.display() in relax, I get the table with all the 
> > data which is as follows...
> >
> > Diffusion type   spheroid
> >   tm (s)            4.63577e-09
> >   Diso (rad/s)      3.59523e+07
> >   Da (rad/s)       -3.36136e+07
> >   Dpar (rad/s)      1.35432e+07
> >   Dper (rad/s)      1.35432e+07
> >   Dratio               0.287196
> >   theta (rad)          0.633624
> >   phi (rad)             2.61738
> >   Fixed flag       True
> >
> > What is confusing me is that, even though the Dratio is 0.287196, the 
> > individual Dpar and Dper values are exactly the same! I have seen the same 
> > when I run relax on a complex of the 5 kDa protein and a 1.1 kDa peptide, 
> > where relaxation data was recorded only for the protein.
> >
> > I ran another run, this time using the pdb file containing all the 15 
> > lowest energy structures. Analysis of the same relaxation data with this 
> > structure gives me an ellipsoid diffusion model with following parameters..
> >
> > Diffusion type   ellipsoid
> >   tm (s)           4.63094e-09
> >   Diso (rad/s)     3.59898e+07
> >   Da (rad/s)        2.4722e+07
> >   Dr                  0.475806
> >   Dx (rad/s)       1.59863e+07
> >   Dy (rad/s)        3.9512e+07
> >   Dz (rad/s)       5.24711e+07
> >   alpha (rad)          2.59643
> >   beta (rad)             2.087
> >   gamma (rad)         0.438009
> >   Fixed flag       True
> >
> > I remember reading an old post where Ed mentions that relax is not set up 
> > to carry out analysis for residues with multiple NH bond vectors since it 
> > lies in the model-free theory itself. In the same post it is also 
> > mentioned that if that is the case then relax should give an error. Now, 
> > about 5 residues at the N terminus and 2 at the C terminus of my 43 
> > residue protein are unstructured and show high backbone RMSD. It would be 
> > great if i get some help regarding the understanding of why in such a 
> > case, there was no error given from relax. And also, what measures are to 
> > be taken to run relax analysis on such a protein using the 15 structure 
> > ensemble as an input structure. Is this change from oblate to ellipsoid a 
> > case of over-estimation of the diffusion properties occuring due to highly 
> > flexible termini in the protein?
> >
> > Regards,
> >
> > Vineet
> >
> >
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