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