Re: [modeller_usage] automatic alignment pdb file with gap to the similar complete sequence

[Modeller Caretaker <>]

On 3/22/13 3:09 AM, THUREAU Aurelien wrote:
> I want to fill a PDB files with missing residues.
...
> I just want to optimize by doing _automatically_ the alignment.

We generally recommend creating the alignment manually for simple cases 
like these (it would be easy to script too if you're planning to do this 
for many cases). Global dynamic programming is going to try to make a 
'sensible' alignment, which isn't what you want (since it will minimize 
the huge insertions that you want). You might be able to make it work by 
setting the gap penalties to zero and doing a regular sequence alignment 
(not align2d) but it's probably more trouble than it's worth.

	Ben Webb, Modeller Caretaker
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