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 <edward@xxxxxxxxxxxxx>
wrote:
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
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Re: relax-users Digest, Vol 116, Issue 38