You probably need to assign the chain ID in your alignment file, if the pdb file does contain chain ID (i.e. A). Better to double-check the PIR format in modeller manual.
Xiang (Sean)
On Tue, 1 Jul 2003, truename wrote:
> Hi!Everybody: > Is there anybody who can correct this error for me? > My error messages are as following > __________________________________ > openf5__224_> Open 11 OLD SEQUENTIAL ./1DBG_A.pdb > rdpdb___303E> No atoms were read from the specified input PDB file: > 1) Possibly because an incorrect/non-existent PDB file is specified. > 2) Possibly because the segment is specified incorrectly in the > alignment file or by the TOP variable MODEL_SEGMENT. That is, > the beginning residue number and/or chain id in MODEL_SEGMENT > may not be found in the input PDB file; MODEL_SEGMENT: 1: > To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' > rdabrk__288W> Protein not accepted: 1 > rdabrk__290E> Number of residues in the alignment and pdb files are different: 506 0 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > ___________________________________________________________ > and my top file > ___________________________________________________________ > # Very fast homology modelling by the MODELLER TOP routine 'model'. > > INCLUDE # Include the predefined TOP routines > SET ALNFILE = 'Together2.ali' # alignment filename > SET KNOWNS = '1DBG_A' '1AIR_' # codes of the templates > SET SEQUENCE = 'T0101' # code of the target > SET ATOM_FILES_DIRECTORY ='./:../atom_files' # directories for input atom files > SET STARTING_MODEL = 2 > SET ENDING_MODEL = 2 > > SET OUTPUT_CONTROL = 1 1 1 1 2 > # SET OUTPUT = 'LONG' > SET FINAL_MALIGN3D = 1 > CALL ROUTINE = 'very_fast' # prepare for extremely fast optimization > > CALL ROUTINE = 'model' # do homology modelling > ________________________________________________________________ > My alignment file > ______________________________-- > >P1;1DBG_A > structureX:1DBG_A:1 : :506 : : : : : > ----MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTY-- > -----KDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRA > IQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTD > KITFDQVINLNNTARAIKDGSVGGPGMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGR > CLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQR > FGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFIN > VNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKN > SWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDE > VRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH* > >P1;T0101 > sequence:T0101:1 : :400 : : : : : > ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTI > PYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFD----------FSFPDSQWVQAS--- > --------------YGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHN---- > ----------RNTGLEINNG--GSYNTVINSDAYRNYDPKKNGSMADGFGP-KQKQGPGN > RFVGCRAWENSDDGFDLFDS--PQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQA > VGN-------HRITRSVAFGNVSKGFDQNNNAGGVT---------------VINNTSYKN > GINYGFGSNVQSGQK----------------------HYFRNNVSLSASVTVSNADAKSN > SWDTGPAASASDFVSLDTSL------------------------ATVSRDNDGTLPETSL > FRLSANSKLINAGTKESNISYSGSAPDLGAFERN---* > >P1;1AIR_ > structureX:1AIR_:1 : :353 : : : : : > ---------ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKG---- > -----GAYPLVITYTGNEDSLINAAAAN--------------------ICGQWSKDPRG- > --------------VEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGG- > ----------AKDGDMIRVD--DSPNVWVDHNELFAANHECDGTPDN-----------DT > TFESAVDIKGASNTVTVSYN-----YIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNAR > LPLQ-------RGGLVHAYNNLYTNITGSGLNVRQN------------------GQALIE > NNWFEKAINPVTSRY--------------------------DGKNFGTWVLKGNNITKPA > DFSTYSITWTADTKPYVNAD---------------------------SWTSTGTFPTVAY > N----YSPVSAQCVKDKLPGYAGVGKNLATLTSTACK* > ______________________________________________________ > My PDB files and sequences used in the alignment are all from PDB > > Any help would be appreciated. > > YeBin >