Re: [modeller_usage] Quesion about patch the Terminal residues
To: zhou jinming <>
Subject: Re: [modeller_usage] Quesion about patch the Terminal residues
From: Modeller Caretaker <>
Date: Tue, 27 Mar 2007 09:37:55 -0700
Cc:
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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