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