Re: Relax - model free without a structure/PDB? -- August 19, 2014 - 17:40

Hi Edward,

 Thanks! After realizing that there was also an archive for this list, I
saw that you had answered a similar question by Ji Hun at the Saunders lab
- I think I should have checked there first as well. Hope you had a good
vacation!
 From,
Ryan


On Mon, Aug 18, 2014 at 2:58 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:

> Hi Ryan,
>
> Welcome to the relax mailing lists!  I hope that the links Troels
> posted were of help.  I am now back from holidays, hence the late
> reply.  The problem you have, of not having a PDB file or 3D structure
> has been encountered before.  For example searching the relax users
> mailing list (http://dir.gmane.org/gmane.science.nmr.relax.user), you
> may find:
>
> http://thread.gmane.org/gmane.science.nmr.relax.user/472/focus=476
>
> This was a long time ago, but from memory I made it possible to
> perform a model-free analysis without having 3D structural
> information.  However, you should be very, very careful about
> artificial motions in the spherical diffusion model.  See the
> following for a review of these fatal issues:
>
>     d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
> the model-free problem and the diffusion seeded model-free paradigm.
> Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f)
>
> In summary - if you don't see the motion of the spherical model in the
> local tm model, then it probably isn't real!
>
> For the dipole-diploe interaction, you will need to set this up
> differently.  As I am guessing that you are using the GUI interface,
> just follow the instructions at
>
> http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_relaxation_interactions.html
> .
> You can skip or cancel the unit vector calculation part of the
> dipole-dipole interaction wizard as this will just give a RelaxError.
> But you will then have the dipole-dipole interaction set up.  Note
> that this is performed in the script UI mode in the sample script
> described at
> http://www.nmr-relax.com/manual/Single_model_free_model_script_mode_sample_script.html
> .
> I hope this helps.
>
> Regards,
>
> Edward
>
>
> On 31 July 2014 21:47, Ryan Lo <rhl4vf@xxxxxxxxxxxx> wrote:
> > Hello,
> >
> >  I'm also a new user of Relax.  I have a perhaps silly question.
> >
> >  I'm studying a protein without a structure, and have processed my R1 R2
> > relaxation data at 600 and 800 MHz using Relax. When I move to the
> > Model-free analysis portion, I've followed the manual, and have tried
> > changing the Protocol mode, as suggested:
> >  "However if you are studying a system without a 3D structure,you can
> > execute each individual component of the analysis byclicking on the
> > “Change” button."
> >
> > However, Relax throws an error, saying
> >
> > Missing data.
> > The set up is incomplete.
> > Please check for the following missing information:
> > Interatomic data (for the dipole-dipole interaction)
> >
> > Considering I don't have a PDB to read for the dipolar relaxation input,
> is
> > there a way I can continue? Thank you all very much for your time. I look
> > forward to hearing your response.
> >
> > From,
> > Ryan
> > _______________________________________________
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> >
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