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
Hi,
The ATOM's lines in the pdb file could not have been read. The reason in that if the alignment is to some chain as in the case of 1DBG_A.pdb the line in the alignment should be:
structureX:1DBG_A:1 :A :506 A : : : : : instead of structureX:1DBG_A:1 : :506 : : : : :
good day, Iris.
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 andpdb 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 inthe alignment are all from PDB > > Any help would be appreciated. > > YeBin >
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 >
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sasson iris -
truename -
xiang li