Re: [modeller_usage] can't bond disulfide

Date: Fri, 17 Nov 2006 13:40:24 +0700
From: jitrayut.018@gmail.com
To: jitrayut_018@hotmail.com
Subject: Fwd: can't bond disulfide

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From: ">modeller_usage-owner@salilab.org <"> modeller_usage-owner@salilab.org>
Date: พ.ย. 16, 2006 10:21 หลังเที่ยง
Subject: can't bond disulfide
To: ">jitrayut.018@gmail.com

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From: "jitrayut jitonnom" < ">jitrayut.018@gmail.com>
To: ">modeller_usage@salilab.org
Date: Thu, 16 Nov 2006 22:21:07 +0700
Subject: can't bond disulfide

Dear modeller users,

I want to bond two disulfides (residue 20 and residue 66, res 105 and res 164) by using script below. But i did not bond any disulfides so why ?

these files used to do scripts below are also attached so if anyone can bond the disulfide which i said i will thanks.

Any suggestions will also be thanks.

Jitrayut Jitonnom, Ph.D.(candidate)
Dept. of Chemistry,
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Tel: +66(0)6613-4218
Email: ">jitrayut.018@gmail.com

from modeller.automodel import *
# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class mymodel(automodel):
    def special_patches(self, aln):

        self.patch(residue_type='DISU', residue_ids=('20', '66'))
        self.patch(residue_type='DISU', residue_ids=('105', '164'))
# This is as usual:
log.verbose()
env = environ()
a = automodel(env, alnfile='CD147-mult.ali',
              knowns=('1F97A','1NBQA','1EPFB'), sequence='CD147')
a.starting_model = 1
a.ending_model = 5
a.make()