Dear Mustafa,
Don't fall in multichain scripts etc.
Specify chains in model_mult.py or model_multiple.py from all of your n chains using n different copies of your template, available in the same folder. This will solve purpose for alignment too.
Good Luck
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Wednesday, July 13, 2011 1:46:00 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 98
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Today's Topics:
1. Re: optimize.py (Modeller Caretaker)
2. Re: Modelling of multi-domain protein from oligomeric
template (Modeller Caretaker)
3. Multi-chain modeling (MUSTAFA BUGHIO)
4. Disulphide patch (MUSTAFA BUGHIO)
----------------------------------------------------------------------
Message: 1
Date: Wed, 06 Jul 2011 12:18:04 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] optimize.py
To: MUSTAFA BUGHIO <>
Cc:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 07/06/2011 06:58 AM, MUSTAFA BUGHIO wrote:
> I am trying to do energy minimization step by running optimize.py script
> file but it does not execute every time i tried to run and got the
> following error, i will be thankful if you help me get this problem
> resolved.
>
> IOError: pdbnam_____E> Filename for PDB code not found: hGLR
> Directories: ../atom_files
> Extensions : :.atm:.pdb:.ent:.crd
> (Also tried prepending 'pdb', looking for .Z, .gz, .bz2,
> .7z, .xz,
> and trying PDB-style subdirectories - e.g. ab for
> pdb1abc.ent)
Just like it says, you asked it to open a PDB file called "hGLR" and
told it to look for it in the ../atom_files directory, and it can't find
it in there. Set env.io.atom_files_directory to the directory containing
your PDB file (or remove that line entirely if it's in the same
directory as the script).
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
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------------------------------
Message: 2
Date: Wed, 06 Jul 2011 12:21:23 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Modelling of multi-domain protein from
oligomeric template
To: Chugunov Anton <>
Cc:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 07/06/2011 07:40 AM, Chugunov Anton wrote:
> What I expect, is a single-chain model that consists of four domains,
> each built from respective template's chain according to the alignment.
> What I get (as far as I see from the *.ini file, since no models output
> due to high energy-function) is the first domain followed by a huge
> non-structured loop
If the alignment you posted is the one you're actually using, then you
have aligned DOM 2 through 4 with gaps in your template, so obviously
Modeller has no structure to work with in that region. Remove all of
those gaps from your template so that DOM-2 is aligned with BBBB, DOM-3
with CCCC and DOM-4 with DDDD.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Wed, 13 Jul 2011 13:09:47 +0500
From: MUSTAFA BUGHIO <>
Subject: [modeller_usage] Multi-chain modeling
To:
Message-ID:
<CALHZR27Esm9NCFGUutQku919GY4k01vAMKTv_3-+ObC=u_s+>
Content-Type: text/plain; charset="iso-8859-1"
Dear Modeller
I am trying to develop multichain model using /model-multichain.py file but
as my model is pentamer in nature the example given is for dimer, i dont
know how to make mult-chain.ali file and what i should mention in header
since my template chains are 5 A-E the given example has only 1 :A:74 :B:
option, how should i change the script to run all five chain modelling
together.
plz help
Regards
Mustafa
--
MUSTAFA BUGHIO
Junior Research Fellow
Lab # P-133
Computational Medicinal Chemistry and Drug Design
Panjwani Center For Molecular Medicine and Drug Research, International
Center for Chemical Sciences, University of Karachi, Karachi 75270
Pakistan, +923313425010
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Message: 4
Date: Wed, 13 Jul 2011 13:15:57 +0500
From: MUSTAFA BUGHIO <>
Subject: [modeller_usage] Disulphide patch
To:
Message-ID:
<CALHZR24Tgsmo-DmAQY5NKhVTqKPJKi23Vx+>
Content-Type: text/plain; charset="iso-8859-1"
Dear Modeller
This is with reference to the python file ***
examples/commands/patch_disulfides.py<http://salilab.org/modeller/examples/commands/patch_disulfides.py>i
am building a model with two disulphide bridges position:
*138 CYS -> 152 CYS
198 CYS -> 209 CYS
where as the python file contains example for one disulphide bridge, how can
i edit the file or there is any other procedure to solve this problem.
Should i use above mentioned py file or patch.py for assigning developing
disulphide bridge.
Regards
--
MUSTAFA BUGHIO
Junior Research Fellow
Lab # P-133
Computational Medicinal Chemistry and Drug Design
Panjwani Center For Molecular Medicine and Drug Research, International
Center for Chemical Sciences, University of Karachi, Karachi 75270
Pakistan, +923313425010
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