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Re: Incorrect PDB file



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
>