On 30 September 2016 at 10:16, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > On 29 September 2016 at 09:55, Gary Thompson <g.s.thomp...@leeds.ac.uk> wrote: >> Hi Sam >> >> have you tried with only one set of coordinates (i presume these are both >> homo dimers with some form of symetry plane or axis? > > Looking at the file attached to https://gna.org/bugs/?25133, the > problem is at the start of the script: > > """ > relax> structure.read_pdb(file='cluster1_12.pdb', dir=None, > read_mol=None, set_mol_name='hRGS4', read_model=None, > set_model_num=None, alt_loc=None, verbosity=1, merge=False) > > Internal relax PDB parser. > Opening the file 'cluster1_12.pdb' for reading. > Adding molecule 'hRGS4' (from the original molecule number 1). > Merging with molecule 'hRGS4' (from the original molecule number 2). > """ > > Note the text "Merging". This is because you are setting all > molecules in the PDB file to the single molecule name "hRGS4". What > you need to do is read a single molecule (via the 'read_mol' > argument). Note Gary's text about symmetry. If you have a homo dimer > without symmetry, there is absolutely no theory on the planet > currently developed to handle relaxation data in this situation.
Running the RGS4_modelfree_sample_script.py script with the "read_mol=1" argument for the structure.read_pdb user function causes the IndexError to go away. Unfortunately I don't have the time to investigate and turn this into a self-explanatory check and RelaxError yet. Cheers, Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
