Dear sir/madam, I have a problem with modeller and probably you can help me. I want to do protein structure modelling. I have the sequence of a bacterium protein, and it's known that it has tree identical chains like this: MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ*
I don't really know what can I do to avoid the chains overlap. I have tried to copy the sequence three times but it doesn't work. This is what I did:
MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA AFEKINEARS PLLPQLGLGA DYTYTSGFRD YKDQNSNVTS GSLQLTQVLF DMSKWRALTL QEKQAGIQDV TYQTDQQTLI LNTATAYFKG LAAIDTLSYT EAQKQAIYRQ LDQTTQRFNV GLGAITDVQN ARSQYDAVLA NEVTARNDLD NAPQKLRQGT GNYYPELGSP NGKGFKTNKP QAVNALLKEA ESRNLSLLQA RLSQDLAREQ IPQAQDGHLP TLNLNASSGV SNNRYSGSKS ISQDADVGQN KIGLSFSLPL YQGGMVNSQV KQAQYNFVGA SEQLESAHRS VVQTVRSSFN NVNASISSIN AYKQAVVSAQ SSLDAMEAGY SVGTRTIVDV LDATTTLYNA KQQLSNARYN YLINELNIKS ALGTLNEQDL VALNNTLGKS IPTSPDSVAP ENPQQDASAD GYSNTAAAKP ASARTTQTSG SNPFRQ*
Could you help me, please? I need to know how can I find a solution and I don't know the way to get it. When I copy the sequence three times, the program don't distinguish the three chains, and it overlap them. I'm waiting for your reply. Thank you very much.
Ester
Ester Fusté Domínguez wrote: > I have a problem with modeller and probably you can help me. > I want to do protein structure modelling. > I have the sequence of a bacterium protein, and it's known that it has > tree identical chains like this: > MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA ...
It would be more helpful if you could show the actual Modeller inputs (i.e. Python script, and alignment file) you're using. I'm assuming this sequence isn't the actual alignment file you're passing to Modeller - for one thing, Modeller sequences must not have spaces in them. And what are the templates you're using? Do they also have three identical chains, or are you trying to build a trimer from a monomer template?
> I don't really know what can I do to avoid the chains overlap. > I have tried to copy the sequence three times but it doesn't work.
I'm not sure what you mean by "chains overlap". But what you are certainly missing in your sequence are chain breaks - '/' characters - which will prevent the termini in adjacent chains from being bonded. See also http://salilab.org/modeller/9v1/manual/node27.html
When you say "doesn't work" what is the error message you receive?
Ben Webb, Modeller Caretaker
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Ester Fusté Domínguez -
Modeller Caretaker