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Re: PDB format and NMR models



Hi,

have you tried to rename your structure file, i.e. from dva.atm to 
dva.pdb? 

ralf


=======================================
Dr. Ralf Schmid
Institute of Cell and Molecular Biology
The University of Edinburgh
King's Buildings
Michael Swann Building 3.14
Edinburgh EH9 3JR





On Mon, 3 Mar 2003, Simon Holton wrote:

> Dear All,
> 
> I am a new user to modeller am having a few teething problems.  I am trying
> to align a sequence against an NMR structure of a related protein but am
> getting an error of
> 
> rdpir___648E> Alignment sequence not found in PDB file:        1  ./dva.atm
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
> 
> 
> The script file is attached below (and I do have a file ./dva.atm)  The
> sequences in alignment and atm files also match exactly.
> 
> >From the manual I was unclear how the options structureX and structureN and
> so wonder whether there are strict formatting requirements for the pdb entry
> (some of the pdb is also attached below).  I edited the NMR model down to
> one solution as I couldn't find any info on how modeller deals with NMR
> models. As a related question if anybody could shed some light on how NMR
> models are dealt with differently (if at all) compared to say
> crystallographic models and if multiple NMR models of the same structure can
> be used as models without inputting each as a separate structure I would be
> very interested to hear,
> 
> 
> 
> 
> Thanks in Advance for your help
> 
> Simon Holton,
> 
> 
> More ./aln.ali
> >P1;dva
> structureX:dva:::::::
> QEKEAIERLKALGFPESLVIQAYFACEKNENLAANFLLSQNFDDE*
> >P1;uba
> sequence:uba:::::::
> ERYEHQLRQLNDMGFFDFDRNVAAKRRSGGSVQALDSLLNGDV--*
> 
> 
> 
> More ./dva.atm
> 
> ATOM      1  N   GLN A   1      28.264  11.297   6.524  1.00  0.00
> ATOM      2  CA  GLN A   1      29.549  11.974   6.654  1.00  0.00
> ATOM      3  C   GLN A   1      30.660  11.272   5.855  1.00  0.00
> ATOM      4  O   GLN A   1      31.702  11.865   5.591  1.00  0.00
> ATOM      5  CB  GLN A   1      29.969  12.114   8.135  1.00  0.00
> ATOM      6  CG  GLN A   1      29.478  13.426   8.785  1.00  0.00
> ATOM      7  CD  GLN A   1      30.626  14.303   9.317  1.00  0.00
> ATOM      8  OE1 GLN A   1      30.822  15.438   8.887  1.00  0.00
> ATOM      9  NE2 GLN A   1      31.337  13.724  10.301  1.00  0.00
> ATOM     10  H   GLN A   1      28.069  11.159   5.506  1.00  0.00
> ATOM     11  HA  GLN A   1      29.432  12.960   6.205  1.00  0.00
> ATOM     12 1HB  GLN A   1      29.572  11.270   8.700  1.00  0.00
> ATOM     13 2HB  GLN A   1      31.051  12.022   8.242  1.00  0.00
> ATOM     14 1HG  GLN A   1      28.910  14.034   8.087  1.00  0.00
> ATOM     15 2HG  GLN A   1      28.785  13.199   9.596  1.00  0.00
> ATOM     16 1HE2 GLN A   1      31.194  12.757  10.532  1.00  0.00
> ATOM     17 2HE2 GLN A   1      32.016  14.236  10.824  1.00  0.00
> 
> More ./model_default.top
> # Homology modelling by the MODELLER TOP routine 'model'.
> 
> INCLUDE                             # Include the predefined TOP routines
> 
> SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log file
> SET ALNFILE  = 'aln.ali'      # alignment filename
> SET KNOWNS   = 'dva'               # codes of the templates
> SET SEQUENCE = 'uba'               # code of the target
> SET ATOM_FILES_DIRECTORY = './'
> SET STARTING_MODEL= 1               # index of the first model
> SET ENDING_MODEL  = 2               # index of the last model
>                                     # (determines how many models to
> calculate)
> CALL ROUTINE = 'model'              # do homology modelling
> 
> 
> 
> 
> **************************************************************
> 
> Dr. Simon Holton 
> Laboratory of Molecular Biophysics,
> Rex Richards Building,
> Department of Biochemistry,
> University of Oxford
> South Parks Road 
> Oxford 
> 
> Tel:    01865 275379
> Fax:   01865 275182
> 
> **************************************************************
> 
>