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

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

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

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