Thanks Ed ! Another similar would maybe ease life of users without PDB or with small proteins... We could add the possibility of not having any file for unresolved residues... The lines : ============= # The file containing the list of unresolved residues to exclude from the analysis. UNRES = 'unresolved' ============= could become : ============= # The file containing the list of unresolved residues to exclude from the analysis (set this to None if no residue is to be excluded). UNRES = 'None' ============= and the lines : ============= # Unselect unresolved residues. unselect.read(name, file=UNRES) ============= could become : ============= # Unselect unresolved residues. if not UNRES: unselect.read(name, file=UNRES) ============= This would avoid using an empty file for (non existant) unresolved residues or commenting 2 different lines in the code... If you agree, I could make the change right away... Ciao ! Sébastien Edward d'Auvergne wrote: Done! See https://mail.gna.org/public/relax-commits/2008-01/msg00376.html. The current version of the script in the 1.2 line will now properly handle not having a PDB file if you set the value of PDB_FILE to None. Nevertheless, I would be very careful with the conclusions. If there are regions appearing to exhibit chemical exchange or slow nanosecond motions - check very carefully that these motions are also present in the local tm model MI results. If not, there is a good chance that you have artificial motions! Regards, Edward On Jan 10, 2008 8:20 PM, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:Hi, I am now helping someone to start with relax and got into a question about the full_analysis.py script. In the full_analysis.py script, the following code appears at line 550 : # Load the PDB file. if not local_tm: pdb(name, PDB_FILE) For a local tm, no PDB file is needed. That's logic. However, I would have thought that no pdb file would also be needed for an isotropic diffusion tensor (sphere). Am I right ? Can someone with no 3D structure use the full_analysis.py script to optimize an isotropic diffusion tensor ? Thanks ! Sébastien :) _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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 -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 |