[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

PDB format and NMR models



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

**************************************************************