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)
> >
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>
Re: [bug #7241] Problem with reading RNA PDBs