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Re: [modeller_usage] Bad Model

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'
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Joao Renato Carvalho Muniz       < e-mail:  >
Laboratorio de Cristalografia de Proteinas e Biologia Estrutural e
Centro de Biotecnologia Molecular Estrutural - CEPID/FAPESP
Instituto de Fisica de Sao Carlos
Universidade de Sao Paulo
Av. do Trabalhador Saocarlense, 400
Centro - Caixa Postal 369 13560-970 - Sao Carlos - SP 
BRASIL
Phone: ++55 16 3373.9868
FAX:   ++55 16 3373.9881
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