Modelling a heterodimeric structure using heterodimeric template
Dear Sir/Madam,
I am modelling a heterodimeric structure from a heterodimeric template. I tried modelling it using separate chains but I am facing difficulty in building the complex. Is it possible to build a model using the complex structure as a whole (I did see a mention of using "/" as a chain separater in your archives for a homodimer)? If so, how do I specify the regions to be modelled?I have put an example of the regions:
query chain 1 length: 878 region aligning:1-827 template: chain B; actual region in pdb: 362-1335 ; region aligning;427-1335
query chain 2: length: 901 length aligning:59-848 template: chain A; actual region in pdb:1-855; length aligning;150-854
Awaiting your response. Thanking you, RAKSHAMBIKAI R PhD student Prof N Srinivasan's lab MBU,IISc Ph:080-22932837
On 8/17/12 6:59 AM, Rakshambikai R wrote: > I am modelling a heterodimeric structure from a heterodimeric template. I tried > modelling it using separate chains but I am facing difficulty in building the > complex. Is it possible to build a model using the complex structure as a whole > (I did see a mention of using "/" as a chain separater in your archives for a > homodimer)?
Yes. Look at the example in the manual: http://salilab.org/modeller/9.10/manual/node28.html
A heterodimer would be exactly the same, except that you don't include the symmetry restraint.
> If so, how do I specify the regions to be modelled?
It's exactly the same as for single chain models. Your alignment file tells Modeller the range of residues to read from the PDB file. Modeller reads PDB files line by line, so most likely you'll want to tell it to start at the first residue in chain A and stop at the last residue in chain B, just like the example in the manual.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Rakshambikai R