Re: [modeller_usage] one question about merging two proteins into one

[Modeller Caretaker <>]

On 4/26/11 2:50 PM, zhangliqun wrote:
> I tried to merge two protein dimers into one dimer, with only 7 residues
> overlapped in each monomer.
...
> a = automodel(env, alnfile = 'alignment.ali',
> knowns = 'pl5t', sequence = 'plxd')

Since you have two templates, you need two 'knowns' here, i.e.

a = automodel(env, alnfile = 'alignment.ali',
              knowns = ('pl5t', 'pbjm'),
              sequence = 'plxd')

> Above files are built based on instructions online. But when I used
> mod9v8 obtain_structure.py command, I got following error message:
...
> parse_pir__E> Invalid PIR file header line: sequence:plxd
> There should be 10 fields separated by colons, :
> This line actually contains 2 fields.

Just like it says, the the line starting with 'sequence:plxd' in your 
alignment file is not in the correct format. It should actually look like:

sequence:plxd::::::::

	Ben Webb, Modeller Caretaker
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