MII-MV of full_analysis.py with RNA -- September 28, 2006 - 19:58

Hello again,

I'm having some problems getting relax to read in an RNA pdb.  When I use MI (local_tm) it runs perfectly well, but when I go to sphere, it crashes.

I realized quickly that I needed to tell the pdb input function to look for different nuclei so I changed those lines (380 and 174) in full_analysis.py to:

pdb(name, 'etar_au22_phage_df_pt.pdb', heteronuc='N1', proton='H1')


And that helped, but still it crashed.  I was using a pdb where the residues weren't numbered sequentially, so I tried one where they were sequential and that didn't help.  I simplified the PDB and input down to one residue and it still failed.  Using the Input and PDB I have below, this is my full result when setting 
self.diff_model = 'sphere':

$ python relax full_analysis.py

relax> run.create(run='sphere', run_type='mf')

relax> results.read(run='sphere', file='results', dir='local_tm/aic', format='columnar')
Opening the file 'local_tm/aic/results.bz2' for reading.

relax> model_free.remove_tm(run='sphere', res_num=None)

relax> pdb(run='sphere', file='etar_au22_phage_df_pt.pdb', dir=None, model=None, heteronuc='N1', proton='H1', load_seq=1)
Loading all structures from the PDB file.
Structure('etar_au22_phage_df_pt.pdb', model=1):
  Nucleotide chain of length 1


Calculating unit XH vectors.


Structure 1

Traceback (most recent call last):
  File "relax", line 458, in ?
    Relax()
  File "relax", line 170, in __init__
    self.interpreter.run()
  File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 213, in run
    run_script(intro=self.relax.intro_string, local=self.local, script_file=self.relax.script_file, quit=1)
  File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 388, in run_script
    console.interact
(intro, local, script_file, quit)
  File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 340, in interact_script
    execfile(script_file, local)
  File "full_analysis.py", line 412, in ?
    Main()
  File "full_analysis.py", line 174, in __init__
    pdb(name, 'etar_au22_phage_df_pt.pdb', heteronuc='N1', proton='H1')
  File "/local/home/viochem/relax_1.2.7/prompt/pdb.py", line 129, in pdb
    self.relax.generic.pdb.load(run=run, file=file, dir=dir, model=model, heteronuc=heteronuc, proton=proton, load_seq=load_seq)
  File "/local/home/viochem/relax_1.2.7/generic_fns/pdb.py", line 198, in load
    self.vectors()
  File "/local/home/viochem/relax_1.2.7/generic_fns/pdb.py", line 229, in vectors
    pdb_residues = self.relax.data.pdb[self.run].structures[i].peptide_chains[0].residues
IndexError: list index out of range


Is this a bug, or is there something else I'm forgetting?  I find the second to last line a little curious (pdb_residues = ... .peptide_chains[0]... ) since I'm using a nucleic acid.


So, In relation to this, what are the important features of the input pdb?

1) sequential numbering of the residues
2) sequential numbering of the atoms
3) spacing of the columns
4) first line (MODEL      #)
5) Last two lines (ENDMDL and END)
6) other ...

Thanks for all of the help.
Alex Hansen



My Simplified Input Data:

R1:
Num  Name   Value    Error                         
1    G     0.738       0.022

R2:
Num  Name   Value    Error                         
1    G     23.74       0.33

NOE:
Num  Name   Value    Error                         
1    G     0.686    0.018


My Simplified PDB - Columns match up perfectly with "pdb" found in test_suite/data/model_free/S2_0.9..etc./

MODEL        1
ATOM      1  N1  G       1      -1.768  -8.924 -45.646  1.00  0.00           N
ATOM      2  H1  G       1      -1.267  -8.064 -45.271  1.00  0.00           H
ENDMDL
END