[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] can't bond disulfide









Date: Fri, 17 Nov 2006 13:40:24 +0700
From:
To:
Subject: Fwd: can't bond disulfide



---------- Forwarded message ----------
From: "> <"> >
Date: ¾.Â. 16, 2006 10:21 ËÅѧà·Õè§
Subject: can't bond disulfide
To: ">

You are not allowed to post to this mailing list, and your message has
been automatically rejected.  If you think that your messages are
being rejected in error, contact the mailing list owner at
">.


 


---------- ¨´ËÁÒ·Õè¶Ù¡Ê觵èÍ ----------
From: "jitrayut jitonnom" < ">>
To: ">
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:
">
 
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()





Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. Try it!