Hi there,
I am trying to model a multichain protein (homodimer) using 2 templates. I have two issues,
Currently my .pir file looks like this
>P1;seq1
sequence:seq1:1:A:1224:A:::: xxxx/
xxxx*
>P1;template1.pdb
structureX:template1.pdb:40:A:651:B:41:B:648:xxxx/xxxx*
>P1;template2.pdb
structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:xxxx/-------/
>P1;template2.pdb
structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:-------/xxxx*
Firstly, my template 1 I am using both chain A and chain B, they have slightly different missing residues in the template but thats fine.For template 2 I cant put them under the same header, modeller doesn't seem to understand that I want to use chain B of template 2 for both chain A and B of my target so I specified it separately - it seems to work fine though with this setup.
Unfortunately when I try add HETATM information ".." at the end of my target and template 1 and 2 gaps "--" for template 2 modeller says the whole sequence is out of alignment suddenly. I have specific HETATM=true in my script so it reads that part fine.
My alignment looks like this but does not work? Am I missing some obvious?
>P1;seq1
sequence:seq1:1:A:1224:A:::: xxxx../
xxxx..*
>P1;template1.pdb
structureX:template1.pdb:40:A:651:B:41:B:648:xxxx../xxxx..*
>P1;template2.pdb
structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:xxxx--/---------/
>P1;template2.pdb
structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:---------/xxxx--*
RegardsKyle
