So, I'm attempting this model_free.py fix, but I don't think it's as straightforward as you say. My first thought was that the nucleus and pdb reads were only occuring once before the data loop and, since there's more than one nucleus/residue type, that should be included in the loop. Therefore, I copied this:
# Nucleus.
nucleus = self.relax.generic.nuclei.find_nucleus()
# PDB.
pdb = None
pdb_model = None
pdb_heteronuc = None
pdb_proton = None
if self.relax.data.pdb.has_key(self.run):
pdb = self.relax.data.pdb[self.run].file_name
pdb_model = self.relax.data.pdb[self.run].model
pdb_heteronuc = self.relax.data.pdb[self.run].heteronuc
pdb_proton = self.relax.data.pdb[self.run].proton
Into the 'Loop over the sequence' but this didn't work. I then manually read in my pdb and executed some pdb.read and pdb.vector commands to see what those lines are reading and confirmed that pdb.read() doesn't import anything about protons or heteronuclei. Those are only assigned with the pdb.vectors() lines in full_analysis.py. Now, you had suggested that, for me to read in multiple nuclei, I should load the pdb like this:
# Load the PDB file.
pdb.read(name,'my_pdb.pdb')
pdb.vectors(name, heteronuc='N1', proton='H1', res_name='G')
pdb.vectors(name, heteronuc='N3', proton='H3', res_name='U')
While I believe this does read in the different vector types, it ulimately assignes heteronuc to 'N3' and proton to 'H3', writing over the first vector call. Is there another place to pull the nucleus information from for a given row of input data? Can I call the nucleus straight from the input data? How can I be sure that pdb.vectors are matching everything up correctly in calculating relaxation? Where is the list of pdb.vectors stored? What information is stored with each pdb vector (orientation, bond length, nuclei, etc.)? Sorry for all of the remedial questions.
As for read_xxxxx, will this be read_columnar_results or one of the other read_columnar functions? Thanks for all of the help.
Alex
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