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 > <[EMAIL PROTECTED]> 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: >>> <[EMAIL PROTECTED]>). >>> >>> * 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: >>> <[EMAIL PROTECTED]>). >>> >>> * 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: >>> <[EMAIL PROTECTED]>). >>> >>> * 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: >>> <[EMAIL PROTECTED]>). >>> >>> * 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: >>> <[EMAIL PROTECTED]>). >>> >>> >>> 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 >>> <[EMAIL PROTECTED]> 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) >>>> >>>> This is the relax-users mailing list >>>> [email protected] >>>> >>>> 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 >>>> >> >> _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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
