Hi Gary, There is only a monomer version of it on pdb, so if you mean it in that sense, yes. I obtained results from it; however the S^2 were very high, but I attributed this to having data for a dimer, but using a monomer pdb file. If you mean have I tried to just delete set B from the pdb file I uploaded, I have not attempted that. So I am a bit confused here, so if I add read_mol=1 instead of my read_mol=0, it'll only read set A? Assuming symmetry, relax will automatically calculate and determine set B?
Sincerely, Sam On Fri, Sep 30, 2016 at 1:26 AM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > 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 > _______________________________________________ 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
