Re: [bug #7241] Problem with reading RNA PDBs -- September 30, 2006 - 15:46

No, sorry.  I think I forgot to select options above when I submitted it.  My bad.

Alex

On 9/30/06, Edward d'Auvergne < edward.dauvergne@xxxxxxxxx> wrote:

Alex, did you mean for this bug to be set to 'private' rather than
'public'?  The bug report is forwarded to the public relax-devel
mailing list anyway.

Edward


On 9/30/06, Alex Hansen <NO-REPLY.INVALID-ADDRESS@xxxxxxx > wrote:
>
> URL:
>   <http://gna.org/bugs/?7241>
>
>                  Summary: Problem with reading RNA PDBs
>                  Project: relax
>             Submitted by: viochemist
>             Submitted on: Friday 09/29/2006 at 17:23
>                 Category: None
>                 Priority: 5 - Normal
>                 Severity: 4 - Important
>                   Status: None
>                  Privacy: Private
>              Assigned to: None
>          Originator Name:
>         Originator Email:
>              Open/Closed: Open
>                  Release: 1.2.7
>         Operating System: GNU/Linux
>
>     _______________________________________________________
>
> Details:
>
> Full post at https://mail.gna.org/public/relax-users/2006-09/msg00041.html
>
> <481156b20609281057o4fe80f47wc1dda6ea6516498d@xxxxxxxxxxxxxx >
>
> See below for pdb and input.
>
> Lines changed in full_analysis.py:
>
> 128:  'sphere'
> 174:  pdb(name, 'etar.pdb', heteronuc='N1', proton='H1')
> 380:  pdb(name, ' etar.pdb', heteronuc='N1', proton='H1')
>
> $ python relax full_analysis.py
>
> Results:
>
>
> 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.pdb', dir=None, model=None,
> heteronuc='N1', proton='H1', load_seq=1)
> Loading all structures from the PDB file.
> Structure('etar.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.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
>
> ==================
> Simplify the PDB
> ==================
>
> Identical output.
>
>
> Curious line is at the end where it says:
> self.relax.data.pdb[self.run].structures[i].peptide_chains[0].residues
>
>
>
>
> ************
> My Input
> ************
> 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
>
>
> *******************
>  whole residue PDB
> *******************
>
> etar.pdb
>
> MODEL        1
> ATOM      1  P   G       1      -2.918 - 16.615 -49.930  1.00  0.00
> P
> ATOM      2  O1P G       1      -3.505 -17.162 -51.178  1.00  0.00
> O
> ATOM      3  O2P G       1      -1.490 -16.217 -50.016  1.00  0.00
> O
> ATOM      4  O5' G       1      - 3.782 -15.376 -49.413  1.00  0.00
> O
> ATOM      5  O3' G       1      -6.236 -12.842 -50.659  1.00  0.00
> O
> ATOM      6  C1' G       1      -5.187 -12.610 -47.168  1.00  0.00
> C
> ATOM      7  C2' G       1      - 5.658 -11.918 -48.451  1.00  0.00
> C
> ATOM      8  C3' G       1      -5.445 -13.010 -49.490  1.00  0.00
> C
> ATOM      9  C4' G       1      -5.829 -14.263 -48.722  1.00  0.00
> C
> ATOM     10  C5' G       1      - 5.195 -15.566 -49.213  1.00  0.00
> C
> ATOM     11  O4' G       1      -5.357 -14.014 -47.368  1.00  0.00
> O
> ATOM     12  O2' G       1      -7.043 -11.646 -48.287  1.00  0.00
> O
> ATOM     13  N2  G       1      - 3.764  -7.849 -44.958  1.00  0.00
> N
> ATOM     14  O6  G       1       0.310  -9.848 -46.253  1.00  0.00
> O
> ATOM     15  C6  G       1      -0.956  -9.976 -46.221  1.00  0.00
> C
> ATOM     16  C5  G       1      - 1.781 -11.085 -46.692  1.00  0.00
> C
> ATOM     17  N7  G       1      -1.395 -12.320 -47.327  1.00  0.00
> N
> ATOM     18  C8  G       1      -2.570 -12.950 -47.544  1.00  0.00
> C
> ATOM     19  N9  G       1      - 3.710 -12.226 -47.102  1.00  0.00
> N
> ATOM     20  C4  G       1      -3.184 -11.015 -46.550  1.00  0.00
> C
> ATOM     21  N3  G       1      -3.964  -9.991 -45.989  1.00  0.00
> N
> ATOM     22  C2  G       1      - 3.196  -8.955 -45.542  1.00  0.00
> C
> ATOM     23  N1  G       1      -1.768  -8.924 -45.646  1.00  0.00
> N
> ATOM     24  H1' G       1      -5.799 -12.337 -46.307  1.00  0.00
> H
> ATOM     25  H2' G       1      - 5.074 -11.028 -48.681  1.00  0.00
> H
> ATOM     26  H3' G       1      -4.411 -13.056 -49.833  1.00  0.00
> H
> ATOM     27  H4' G       1      -6.911 -14.367 -48.796  1.00  0.00
> H
> ATOM     28 1H5' G       1      - 5.363 -16.346 -48.472  1.00  0.00
> H
> ATOM     29 2H5' G       1      -5.663 -15.858 -50.154  1.00  0.00
> H
> ATOM     30 HO2' G       1      -7.555 -12.532 -48.168  1.00  0.00
> H
> ATOM     31 1H2  G       1      - 4.818  -7.792 -44.843  1.00  0.00
> H
> ATOM     32 2H2  G       1      -3.151  -7.049 -44.622  1.00  0.00
> H
> ATOM     33  H8  G       1      -2.640 -13.960 -48.032  1.00  0.00
> H
> ATOM     34  H1  G       1      - 1.267  -8.064 -45.271  1.00  0.00
> H
> ENDMDL
> END
>
>
> ****************
>  Simplified PDB
> ****************
>
> MODEL        1
> ATOM     23  N1  G       1      - 1.768  -8.924 -45.646  1.00  0.00
> N
> ATOM     34  H1  G       1      -1.267  -8.064 -45.271  1.00  0.00
> H
> ENDMDL
> END
>
>
>
>
>
>
>
>
>
>     _______________________________________________________
>
> Reply to this item at:
>
>   <http://gna.org/bugs/?7241>
>
> _______________________________________________
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>   http://gna.org/
>
>
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