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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Dear A R
Try to put this line in your .top file:
SET DEVIATION = 4.0 # the amount of randomization of the initial model # must be > 0 if different final models are wanted;
Good luck
Joao Renato
A R wrote:
>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 >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >http://salilab.org/mailman/listinfo/modeller_usage > > >
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A R -
Joao Renato Carvalho Muniz