Re: [modeller_usage] Heterodimer modeling

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 6/11/12 10:03 AM, Xiongzhuo Gao wrote:
> I'm building a heterodimer with a homodimer template. I have the
> template pdb file (dimer.pdb) and the sequence file of the heterodimer
> (hetero.ali).
...
> The following is the script I used for alignment:
...
> mdl = model(env, file='dimer', model_segment=('FIRST:A','LAST:A'))

You have asked Modeller to read only one chain of the dimer (the A 
chain), so it has quite happily gone and done that, then aligned your 
sequence to it. ;) Change LAST:A to LAST:B (or remove model_segment 
entirely, which will have Modeller read the entire PDB file).

Note that Modeller's alignment functions ignore chain breaks. So your 
final alignment might need some manual adjustment to get the chain break 
in the template to line up with your query sequence.

	Ben Webb, Modeller Caretaker
--
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