Re: relax 1.3: run.create error -- January 24, 2008 - 20:02

No, there's no need to output the PDB file.  The TNS residue of this
new PDB file is a synthetic construct used to represent the tensor.
It is oriented in the frame of the PDB you supplied to relax.  You can
then use relax together with Pymol to display this TNS residue as a
spherical, spheroidal, or ellipsoidal object (this is what the end of
the 'diff_tensor_pdb.py' tries to do).

Regards,

Edward


On Jan 24, 2008 6:18 PM, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
> Thanks for the reply.  Is there a way to output a PDB file that is
> rotated/translated to the diffusion frame?  The 'diff_tensor_pdb.py'
> script seems to output only a subset of atoms to a residue called 'TNS'.
>
> Thanks again,
> Doug
>
>
>
> On Jan 24, 2008, at 11:16 AM, Edward d'Auvergne wrote:
>
> > Hi,
> >
> > The 'diff_tensor_pdb.py' script has no chance of currently running on
> > the 1.3 repository line code!  The reason is because I haven't
> > migrated all of that code to the new relax design.  Hence the user
> > scripts still have the 'run' name present.  If you grep the source
> > code, you'll see that there are thousands of places where the word
> > 'run' appears.  Once the redesign is finished, there will be zero.
> > This is a long and tedious process for me, so it will take a while.
> > So as this code is half complete, if you decide to use it please
> > expect that everything will be broken (this is, of course, not true as
> > the test suite can confirm).
> >
> > You can, however, use this script with relax version 1.3.0 which is
> > downloadable from http://nmr-relax.com.  This version was released
> > prior to the redesign and almost everything should work.  I'm assuming
> > this all relates to my response at
> > https://mail.gna.org/public/relax-users/2007-12/msg00005.html (which
> > is part of the thread started by your post at
> > https://mail.gna.org/public/relax-users/2007-12/msg00001.html).
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On Jan 24, 2008 4:22 PM, Douglas Kojetin
> > <douglas.kojetin@xxxxxxxxx> wrote:
> > > Hi Edward,
> > >
> > > Thanks for the email.  I wanted to use the 1.3 branch to utilize the
> > > script 'diff_tensor_pdb.py' with analysis output files from the 1.2
> > > branch -- that script (and apparently all of the other scripts in the
> > > sample_scripts directory) still uses 'run' instead of 'pipe', etc.
> > >
> > > Thanks,
> > > Doug
> > >
> > >
> > >
> > > On Jan 24, 2008, at 10:18 AM, Edward d'Auvergne wrote:
> > >
> > > > Hi,
> > > >
> > > > The problem is simply differences between the stable 1.2 versions
> > > > and
> > > > the unstable 1.3 line.  In the development of relax 1.3, many of the
> > > > user functions have been renamed.  There has also been a significant
> > > > redesign of relax.  For full details, have a look at the following
> > > > links and the threads that they start:
> > > >
> > > > * The parent message 'Redesign of the relax data model:  A HOWTO for
> > > > breaking relax.' located at
> > > > https://mail.gna.org/public/relax-devel/2006-10/msg00053.html
> > > > (Message-id:
> > > > <1160550133.9523.54.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
> > > >
> > > > * Section 1 'Redesign of the relax data model:  1.  Why change?'
> > > > located at https://mail.gna.org/public/relax-devel/2006-10/
> > > > msg00054.html
> > > > (Message-id:
> > > > <1160551172.9523.60.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
> > > >
> > > > * Section 2 'Subject: Redesign of the relax data model:  2.  A
> > > > new run
> > > > concept' located at
> > > > https://mail.gna.org/public/relax-devel/2006-10/msg00056.html
> > > > (Message-id:
> > > > <1160555137.9523.70.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
> > > >
> > > > * Section 3 'Redesign of the relax data model:  3.  Molecules,
> > > > residues, and spins' located at
> > > > https://mail.gna.org/public/relax-devel/2006-10/msg00057.html
> > > > (Message-id:
> > > > <1160557041.9523.74.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
> > > >
> > > > * Section 4 'Redesign of the relax data model:  4.  Conclusion'
> > > > located at https://mail.gna.org/public/relax-devel/2006-10/
> > > > msg00058.html
> > > > (Message-id:
> > > > <1160557876.9523.79.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
> > > >
> > > >
> > > > Note also that the 1.3 line code is not fully functional yet as this
> > > > redesign has been slow and is still in progress.  But if you do want
> > > > to play with the current code, note that the name 'run' has been
> > > > replaced by the name 'pipe' and that the concept of a data pipe has
> > > > been introduced so that the pipe name is not passed into each user
> > > > function.  That user functions apply automatically to the 'current'
> > > > data pipe in which you are currently sitting.  And that you can
> > > > switch
> > > > between data pipes, merge them, branch them, etc.
> > > >
> > > > Regards,
> > > >
> > > > Edward
> > > >
> > > >
> > > >
> > > > On Jan 24, 2008 3:14 PM, Douglas Kojetin
> > > > <douglas.kojetin@xxxxxxxxx> wrote:
> > > > > Hi All,
> > > > >
> > > > > When trying to use relax 1.3 (current svn version), I see the
> > > > > following error when trying to use run.create():
> > > > >
> > > > > % /usr/local/relax/1.3/relax
> > > > >
> > > > > ImportError: relaxation curve fitting is unavailible, try compiling
> > > > > the C modules.
> > > > >
> > > > >
> > > > >
> > > > >                                       relax repository checkout
> > > > >
> > > > >                            Protein dynamics by NMR relaxation data
> > > > > analysis
> > > > >
> > > > >                               Copyright (C) 2001-2006 Edward
> > > > > d'Auvergne
> > > > >                           Copyright (C) 2006-2008 the relax
> > > > > development team
> > > > >
> > > > > This is free software which you are welcome to modify and
> > > > > redistribute under the conditions of the
> > > > > GNU General Public License (GPL).  This program, including all
> > > > > modules, is licensed under the GPL
> > > > > and comes with absolutely no warranty.  For details type 'GPL'.
> > > > > Assistance in using this program
> > > > > can be accessed by typing 'help'.
> > > > >
> > > > > relax> run.create('test','mf')
> > > > > Traceback (most recent call last):
> > > > >    File "<console>", line 1, in ?
> > > > > NameError: name 'run' is not defined
> > > > > relax>
> > > > >
> > > > >
> > > > >
> > > > > Any ideas about this problem?
> > > > >
> > > > > Thanks,
> > > > > Doug
> > > > >
> > > > > _______________________________________________
> > > > > relax (http://nmr-relax.com)
> > > > >
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