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------ Forwarded Message From: "truename" yb_108@yeah.net Date: Sat, 28 Jun 2003 17:48:51 +0800 (CST) To: "modeller care" modeller-care@salilab.org Subject: Re: your modeller question
Dear Ursula Pieper: Thank you for your reply! How ever both the sequence that I used to align and pdb file are from the PDB.They are exactly corrospondent file for the same protein. The content of p.top are as following ___________________________________________________________________________ # 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 = './:../1DBG_A 1AIR_' # 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 ___________________________________________________________________________ and my p.aln file are as follwing ___________________________________________________________________________ >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* ___________________________________________________________________________ Best Regards
YeBin
Error message:
> However, some difficulties confronted me during my first project of > protein modelling. Do you lend me a hand to solve it? > The error messages are as following: > ________________________________________________ > rdpir____648E>Alignment sequence not found in PDB file: 1 ./1AIR.atm > recover_____E>ERROR_STATUS >=STOP_ON_ERROR: 1 1 > > And p.top and p.ali are included in the attachment > > Thanks a lot! > Best regards > > YeBin > > > ------ End of Forwarded Message >