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It`s alive!!!



Hi to all:

I just made modeller work!!!!

I still don`t know what my problem was, but as I can run the examples just
fine, I figured the problem were my files.
Briefly, I just delete my old files and created them from scratch with
nedit...
My final files looked like this:

(model.top, my script):

 INCLUDE                             # Include the predefined TOP routines
 SET ALNFILE  = 'aln.ali'           # alignment filename
 SET KNOWNS   = '1cx1'               # codes of the templates
 SET SEQUENCE = '1dnj'               # code of the target
 SET ATOM_FILES_DIRECTORY = '../bin/modeller6v2/examples/atom_files/' #
directories
 SET STARTING_MODEL= 1               # index of the first model
 SET ENDING_MODEL  = 2               # index of the last model
                                    # (determines how many models to
calculate)
 SET DEVIATION     = 4.0             # have to be >0 if more than 1 model
 SET RAND_SEED     = -12312          # to have different models from another
TOP file
 CALL ROUTINE = 'model'              # do homology modelling




(aln.ali, my alignment file)
C; First alignment
>P1;1cx1
structureX:1cx1:FIRST:A:LAST:A:template:HCV: 2.50:-1.00
GSVVIVGRIILSGSGSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSK
TLAG
PKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLS-------PRPVSYL
KGSS
GGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVP
AAYA
AQGYKVLVLNPSVAATLGFGAYMSKAHGID------PNIRTGVRTITTGAPVTYSTYGKFLADGGCSGGAYDIIIC
DECH
STDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPHPNIEEVALSNTGEIPFYGKAIPIEAI--RGGRHLIF
CHSK
KKCDELAAKLSGLGINAVAYYRGLDVSVIPT---IGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTF
TIET
TTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAETSVRLRAYLNTPGLPV
CQDH
LEFWESVFTGLTH-IDAHFLSQTKQAGDNFPYLVAYQATVCARAQAPPPSWDQMWKCLIRLKPTLH---GPTPLLY
RLGA
VQNEVTLTHPITKYIMACMSADLEVVT*

>P1;1dnj
sequence:1dnj:FIRST:@:LAST:@:model:dengue: 2.50:-1.00
GSSPILSITISEGSGS----AGVLWDVPSPPPVGKAELEDGAYRIKQRGILGYSQIGAGVYKEGTFHTMWHVTRGA
VLMH
KGKRIEPSWADVKKDLISYGG---GWKLEGEWKEGEEVQVLALE-PGKNPRAVQ-TKPGLFKTNTGTIGAVSLDFS
PGTS
GSPIVDRKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIEDD-------IFRKKRLTIMDLHPGAGKTKRYL
PAIV
REAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPV-RVPNYNLIIM
DEAH
FTDPASIAARGYISTRVEMGE-AAGIFMTATPPGSRDPFPQ-SNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWF
VPSI
KAGNDIAACLRKNGKKVIQLSRKTFDSEYVKTRANDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILT-DGEER
VILA
GPMPVTHSSAAQRRGRIGRNPKNENDQYI---------YMGEPLENDEDCAHWKEAKMLLDNINTPEGIIPSMFEP
EREK
VDAIDGEYRLRGEARKTFVDLMRRG---DLPVWLAYRVAAEGINYADRRWCFDGIKNNQILEE-NVEVEIWTKEGE
RKKL
KPRWLDARIYSDPLALKEFKEFAAGRK*


Hope this helps, Holton...

And thanks to all for your help!!!!

Luis