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Today's Topics:

1. loop optimization in the presence of a ligand (Thijs Beuming)
2. Re: loop optimization in the presence of a ligand
(Modeller Caretaker)
3. Re: modeller_usage Digest, Vol 6, Issue 79 (vidhya sankar)


----------------------------------------------------------------------

Message: 1
Date: Thu, 16 Aug 2007 16:21:11 -0400
From: "Thijs Beuming"
Subject: [modeller_usage] loop optimization in the presence of a
ligand
To: modeller_usage@salilab.org
Message-ID: <5C60D3FA-2EF9-44A4-A613-BA0C09614F12@med.cornell.edu>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Hi,

I am trying to optimize a loop in close proximity to a ligand. For
some reason, the intial models have the ligand present, while the
loop optimized models do not. Hence, there are major clashes between
some of the calculated loops and the ligand. Is it possible to
optimize loops in the presence of the ligand?

My input script:

# Homology modeling by the automodel class
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class

log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this
model in

# directories for input atom files
env.io.atom_files_directory = 'MODELLER'

class mymodel(loopmodel):
def special_restraints(self, aln):
rsr = self.restraints
rsr.add(atom_ids=('CA:189', 'CA:372'),
restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))
rsr.add(atom_ids=('CA:189', 'CA:393'),
restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))
rsr.add(atom_ids=('CA:372', 'CA:393'),
restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))

def special_patches(self, aln):
self.patch(residue_type='DISU', residues=(self.residues['176'],
self.residues
['185']))
def select_loop_atoms(self):
return selection(self.residue_range('378:', '383:'))

a = mymodel(env,
alnfile = 'MODELLER/alignment.pir', # alignment
filename
knowns = 'template', # codes of the
templates
sequence = 'target') # code of the target

a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model

a.loop.starting_model = 1 # First loop model
a.loop.ending_model = 2 # Last loop model

a.make() # do the actual homology modeling

Thanks,

Thijs Beuming




------------------------------

Message: 2
Date: Thu, 16 Aug 2007 16:41:55 -0700
From: Modeller Caretaker
Subject: Re: [modeller_usage] loop optimization in the presence of a
ligand
To: Thijs Beuming
Cc: modeller_usage@salilab.org
Message-ID: <46C4E0C3.5090904@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Thijs Beuming wrote:
> I am trying to optimize a loop in close proximity to a ligand. For
> some reason, the intial models have the ligand present, while the
> loop optimized models do not. Hence, there are major clashes between
> some of the calculated loops and the ligand. Is it possible to
> optimize loops in the presence of the ligand?

It's hard to say for sure what your problem is without seeing all of
your input files, but it looks like you haven't turned on env.io.hetatm,
so I don't think you should be seeing ligands in either your regular
models or your loop models.

You can see the restraints that loopmodel builds by looking at the
loop_restraints() method in the modlib/modeller/automodel/loopmodel.py
file. By default it builds stereochemical, phi/psi, and dihedral
restraints, but not the ligand-protein restraints that automodel does.
You could easily fix this to restrain ligands by overriding the
special_restraints() method and calling automodel.nonstd_restraints()
from there. Note however that the ligand-protein restraints may be too
strong to allow your loop to explore much conformational space, so it
may make sense to use weaker or fewer restraints here.

> def special_restraints(self, aln):
> rsr = self.restraints
> rsr.add(atom_ids=('CA:189', 'CA:372'),
> restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))
> rsr.add(atom_ids=('CA:189', 'CA:393'),
> restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))
> rsr.add(atom_ids=('CA:372', 'CA:393'),
> restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))

Note that this way of specifying restraints is error prone and
deprecated. You can see examples of the more robust method at
http://salilab.org/modeller/9v2/manual/node209.html or
http://salilab.org/modeller/tutorial/advanced.html

Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

Message: 3
Date: Fri, 17 Aug 2007 06:25:46 -0700 (PDT)
From: vidhya sankar
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 6, Issue 79
To: modeller_usage@salilab.org
Message-ID: <70610.83508.qm@web51610.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"







can i compare th DOPE score of my mode with dope score of X-ray PDB.?if i can, what should be the DOPE SCORE difference between my model and X-ray PDB in order tobe my model is a reliable model. could you please tell some difference in score value yhanks in advance













modeller_usage-request@salilab.org wrote:
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. Re: superpose.py (vidhya sankar)


----------------------------------------------------------------------

Message: 1
Date: Thu, 16 Aug 2007 01:00:44 -0700 (PDT)
From: vidhya sankar
Subject: Re: [modeller_usage] superpose.py
To: modeller_usage@salilab.org
Message-ID: <467087.77948.qm@web51604.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. upon using this in superpose .py script i have got RMS OF 2.3337 and number of aligned equivalent positions 33 amog 115 residues will it be reliable value ?








modeller_usage-request@salilab.org wrote:
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. Re: log files (vidhya sankar)


----------------------------------------------------------------------

Message: 1
Date: Sat, 11 Aug 2007 04:21:41 -0700 (PDT)
From: vidhya sankar
Subject: Re: [modeller_usage] log files
To: modeller_usage@salilab.org
Message-ID: <267539.63819.qm@web51610.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply






modeller_usage-request@salilab.org wrote:
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modeller_usage@salilab.org

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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. Re: DOPE (Modeller Caretaker)
2. regarding DOPE score (vidhya sankar)
3. regrding superpose.py (vidhya sankar)
4. ref: SUPERPOSE.PY (vidhya sankar)
5. Re: regarding DOPE score (Modeller Caretaker)


----------------------------------------------------------------------

Message: 1
Date: Thu, 09 Aug 2007 12:57:42 -0700
From: Modeller Caretaker
Subject: Re: [modeller_usage] DOPE
To: Ester Fust? Dom?nguez
Cc: modeller_usage@salilab.org
Message-ID: <46BB71B6.8070207@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Ester Fust? Dom?nguez wrote:
> How can I see the DOPE score profile? I don't know how to use
> *assess_dope* command.

There is an example at the end of the basic tutorial at
http://salilab.org/modeller/tutorial/basic.html

Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

Message: 2
Date: Fri, 10 Aug 2007 05:10:48 -0700 (PDT)
From: vidhya sankar
Subject: [modeller_usage] regarding DOPE score
To: modeller_usage@salilab.org
Message-ID: <835492.28231.qm@web51612.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE

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Message: 3
Date: Fri, 10 Aug 2007 06:12:02 -0700 (PDT)
From: vidhya sankar
Subject: [modeller_usage] regrding superpose.py
To: modeller_usage@salilab.org
Message-ID: <748909.620.qm@web51605.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

I have got a RMS and DRMS value of after super position 2.0482 and 1.5631 respectively.is it reliable value? .for 53.85% sequence identity i am expecting your reply

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Message: 4
Date: Fri, 10 Aug 2007 06:13:48 -0700 (PDT)
From: vidhya sankar
Subject: [modeller_usage] ref: SUPERPOSE.PY
To: modeller_usage@salilab.org
Message-ID: <999038.6025.qm@web51601.mail.re2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

I have got a RMS and DRMS value of after super position 2.0482 and 1.5631 respectively.is it reliable value? .for 53.85% sequence identity i am expecting your reply

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Message: 5
Date: Fri, 10 Aug 2007 11:51:17 -0700
From: Modeller Caretaker
Subject: Re: [modeller_usage] regarding DOPE score
To: vidhya sankar
Cc: modeller_usage@salilab.org
Message-ID: <46BCB3A5.6020703@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

vidhya sankar wrote:
> i have got a DOPE score of -41275.816406 is it reliable value ? .how
> can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE

The absolute value is essentially meaningless, so you can use it only to
compare against other models of the same sequence, just like the
Modeller molpdf score. See
http://salilab.org/modeller/9v2/manual/node245.html

Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

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