Hello again:

Still stranded on this one, so I send you my aln file (called 01mod.ali): >P1;1cx1 structure:1cx1 :::::::2.5:0.20 GSVVIVGRIILSGSGSITAYSQQTRGLLGCIITSLTGRDKNQVEGEVQVVSTATQSFLAT CVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYL VTRHADVIPVRRRGDSRGSLLS-------PRPVSYLKGSSGGPLLCPSGHAVGIFRAAVC TRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYA AQGYKVLVLNPSVAATLGFGAYMSKAHGID------PNIRTGVRTITTGAPVTYSTYGKF LADGGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLATATPPGSVTVPH PNIEEVALSNTGEIPFYGKAIPIEAI--RGGRHLIFCHSKKKCDELAAKLSGLGINAVAY YRGLDVSVIPT---IGDVVVVATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIET TTVPQDAVSRSQRRGRTGRGRRGIYRFVTPGERPSGMFDSSVLCECYDAGCAWYELTPAE TSVRLRAYLNTPGLPVCQDHLEFWESVFTGLTH-IDAHFLSQTKQAGDNFPYLVAYQATV CARAQAPPPSWDQMWKCLIRLKPTLH---GPTPLLYRLGAVQNEVTLTHPITKYIMACMS ADLEVVT* >P1;1dnj sequence:1dnj :::::::0.0:0.0 GSSPILSITISEGSGS----AGVLWDVPSPPPVGKAELEDGAYRIKQRGILGYSQIGAGV YKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGG---GWKLEGEWKEGEEVQV LALE-PGKNPRAVQ-TKPGLFKTNTGTIGAVSLDFSPGTSGSPIVDRKGKVVGLYGNGVV TRSGAYVSAIAQTEKSIEDNPEIEDD-------IFRKKRLTIMDLHPGAGKTKRYLPAIV REAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMR LLSPV-RVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGE-AAGIFMTATPPGSRDPFP Q-SNAPIMDEEREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQL SRKTFDSEYVKTRANDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILT-DGEERVILA GPMPVTHSSAAQRRGRIGRNPKNENDQYI---------YMGEPLENDEDCAHWKEAKMLL DNINTPEGIIPSMFEPEREKVDAIDGEYRLRGEARKTFVDLMRRG---DLPVWLAYRVAA EGINYADRRWCFDGIKNNQILEE-NVEVEIWTKEGERKKLKPRWLDARIYSDPLALKEFK EFAAGRK*

Again, the top file goes like this: SET ALNFILE = '01mod.ali' # alignment filename SET KNOWNS = '1cx1' # codes of the templates SET SEQUENCE = '1dnj' # code of the target SET ATOM_FILES_DIRECTORY = './:../PDB:./atom_files' # SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model SET DEVIATION = 4.0 # have to be >0 if more than 1 model SET RAND_SEED = -12312 # CALL ROUTINE = 'model' # do homology modelling

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Let me know if you found something weird on my ali file.... I tried with the MINT script from Dr Andrew, (it complied and run fine) but I still get the same error as with my own script:

check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Thanks in advance,

Luis Rosales