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
>
> **************************************************************
>
>