Dear all, I have to model a chimeric protein of two known sequnces. I have gone through the previous archives and have come across the emails of people who have done it. however, I am confused with how to start the first alignment to get the following alignment file
>P1;proteinA structureX:proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------* >P1;proteinB structureX:proteinB ----------------------------bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb* >P1;chimera sequence:chimera aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb*
is this the .ali file to give for alignment. Which script should I use.
Kindly help with which is the correct script to use.
Thank you
Regards
Ayesha Fatima
QIUP, Ipoh, Perak
On 4/22/18 7:44 AM, Ayesha Fatima wrote:> is this the .ali file to give for alignment.
Yes, an alignment file like that should work fine.
> Which script should I use.
Since it's a chimera most conventional alignment scripts are not going to do the right thing for you, since they will try to make a global alignment of the two proteins, which is precisely not what you want. I would combine them manually, unless you have another structure of a linker region to which both will align.
Ben Webb, Modeller Caretaker
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Ayesha Fatima -
Modeller Caretaker