Re: relax-users Digest, Vol 116, Issue 38 -- September 30, 2016 - 10:26

On 30 September 2016 at 10:16, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> On 29 September 2016 at 09:55, Gary Thompson <G.S.Thompson@xxxxxxxxxxx> 
> 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