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
>