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'
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