Hi, Im trying to model a 58% identity protein with the template, but after alignment, the model.top generates a very different model from the template. Can anybody suggests me what can I change in my model.top to make this better? Thanks.
The alignment is using MALIGN with gap penalties of -600 and -400: >P1;1xxx structureX:1xxx: 5 :A: 689 :B:undefined:undefined:-1.00:-1.00 MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWK DHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVI RTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDE NIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVE IHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLG AVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTI ISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEF VNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPV ILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDH YQEVPKQVQEKLIKGQ* >P1;03883 sequence:03883: : : 696 : :::-1.00:-1.00 -MMARKFELKDYRNIGIMAHIDAGKTTTTERILFHTGKIHKIGETHDGVSQMDWMEQEKERGITITSAATTAFWK GKRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAQSGVEPQTETVWRQATNYSVPRIVYVNKMDKAGANFEASI ESVRTKLNGNAVAIQLNIGAEADFSGLIDLVEMKAYNYDGQKEEIEYEIPIPEDLFEKASQMRLALAEAVADYDE EIFNNLLEEKEILPEQLKAAIRAATITGNFFPVVCGSSFKNKGVKKMIDAVIDYLPSPVDVPPIKAFRDEEEIT- IEASDDQEFSALAFKIMNDPFVGSLTFFRVYSGVLKKGTYIINSTKGKKERVGRILAMHANSREEIDEVRTGDIG AFVGLKDTTTGDSLISEKAKTFVLERMNFPEPVISQSLEPFSKAEIEKLATALQKLANEDPTFKTWTDIETGQTI IAGMGELHLDIIVDRLKREFNVQARVGKPQVSYRETITKSAEVEGKYIKQSGGRGQYGHVWIKFEPNPE-EGFDF IDKIVGGKIPKEYIKSIQKGLEEKMQAGILAGYPLINLRATLFDGSFHEVDSSEMAFKIAASKALSRARDAVGTV LLEPIMDVSVFAPSEYAGDVMGDLSRRRGLVREQETRSDGANVIRGHVPLAEMFGYSTQLRSMTSGRGTYQMQFN HYEIVPKNISDVIVKQRAIKEDD*
the model.top is: INCLUDE SET ALNFILE = 'malign.pir' SET KNOWNS = '1ktv' SET SEQUENCE = '03883' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model'
___________________________________________________________ Moving house? Beach bar in Thailand? New Wardrobe? Win £10k with Yahoo! Mail to make your dream a reality. Get Yahoo! Mail www.yahoo.co.uk/10k