Re: [bug #7241] Problem with reading RNA PDBs -- September 30, 2006 - 17:01

I've attempted to fix bug #7241 (https://gna.org/bugs/?7241).  I've
committed the changes in revision r2591 to the 1.2 line.  The commit
message of those changes is located at
https://mail.gna.org/public/relax-commits/2006-09/msg00064.html
(Message-id: <E1GTgBi-0000R6-4h@xxxxxxxxxxxxxxxxxx>).  Do these
changes fix the issue for your data?  Also, would you have a different
truncated PDB file I could use for debugging?  I may need to do some
testing before closing your bug report.

Thanks,

Edward



On 10/1/06, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> wrote:
> Alex, do you get the following message when using the 'whole residue PDB' 
> data?
>
> 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
>
> I don't get the message 'Nucleotide chain of length 1' and therefore
> can't reproduce the bug.
>
> 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>
> >
> > _______________________________________________
> >   Message sent via/by Gna!
> >   http://gna.org/
> >
> >
> > _______________________________________________
> > relax (http://nmr-relax.com)
> >
> > This is the relax-devel mailing list
> > relax-devel@xxxxxxx
> >
> > To unsubscribe from this list, get a password
> > reminder, or change your subscription options,
> > visit the list information page at
> > https://mail.gna.org/listinfo/relax-devel
> >