Re: How to renumber spins in relax

[Edward d'A. <ed...@do...>]

Hi,

The spin numbers come directly from the PDB file itself.  For example,
here is a PDB line:

ATOM    807  N   GLN A 135      22.572 -18.634  25.569  1.00  1.00           N

If you load this in relax, you'll have an atom name of 'N', an atom
number of 807, a residue name of 'GLN', and a residue number of 135.
If you need to renumber spins, you can use the spin.number user
function (the renumbering is fully documented in the manual, or in the
user function help system).  The spin numbering is very important if
you are working with RNA/DNA or small molecules.  But for proteins,
you can normally safely ignore it.  With a bit of programming skills,
you can use the spin_loop() method to loop over the spins, renumbering
each in the process.  Note that this number will have no effect on
your analysis.

As for importing data without the spin numbers, that is perfectly
fine.  If you have only one spin per residue, you do not need to
supply any spin information at all.  relax will automatically handle
this.  In your case all you will need are three columns with the
residue number, relaxation data, and relaxation error (if you don't
have the error, you can use relax with your original peak height data
to find it), though your current data files can be used unchanged.  I
have designed relax to be as simple as possible while accepting almost
anything you can throw at it.  As for TENSOR, note that you cannot
take a tensor from TENSOR and use it in any of the other model-free
programs as there are 2602 Euler angle conventions, and all model-free
programs known use a convention different from the others.  If you use
the relax GUI, you will also have no need for an initial tensor as I
have developed a protocol which avoids this step.

Regards,

Edward




On 19 April 2012 17:18, Martin Ballaschk <bal...@do...> wrote:
> Hi!
>
> IIRC, the spin number is set according to information in the read pdb file. So the @N of residue number 2 can have e.g. the spin number 18, and so on. Where exactly does this number come from? And is there a way to rename the spin_num to a value that corresponds e.g. to the res_num?
>
> To me it seems more convenient to assign the same number to both spins and residues, as every residue has only one backbone-N. With the somewhat arbitrary spin number it's quite complicated to import external R1, R2 relaxation fits that do not take any spin information from a pdb file into account. (I have a bunch of files I created for TENSOR and these do only contain residue numbers.)
>
> Any hints how to change that would be appreciated. I have no experience in Python but have no problem to learn.
>
> Cheers
> Martin
>
> --
> Martin Ballaschk
> AG Schmieder
> Leibniz-Institut für Molekulare Pharmakologie
> Robert-Rössle-Str. 10
> 13125 Berlin
> bal...@do...
> Tel.: +49-30-94793-234/315
> Büro: A 1.26
> Labor: C 1.10
>
>
> _______________________________________________
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> rel...@do...
>
> 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