Re: [modeller_usage] Quesion about patch the Terminal residues

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

zhou jinming wrote:
> I try to add the terminal residues such as, ACE or CT3,to the N-Term or 
> C-Term, but it always gave the error message, therefore, I come here for 
> help. I used the modeller9,and  the "py" file I using for patch is as 
> following:

Your patches are incorrect. See
http://salilab.org/modeller/9v1/manual/node23.html for an example.

You have:

>     def special_patches(self, aln):
>         # Acetylate the N terminus
>        self.patch(residue_type='ACE', residues='1:')
>         # Standard C terminal patch
>        self.patch(residue_type='CT3', residues='238:')

This should be:

>     def special_patches(self, aln):
>         # Acetylate the N terminus
>        self.patch(residue_type='ACE', residues=self.residues['1:'])
>         # Standard C terminal patch
>        self.patch(residue_type='CT3', residues=self.residues['238:'])

BTW, the standard C terminal patch is CTER, not CT3.

	Ben Webb, Modeller Caretaker
-- 
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