Ajeeta
First of all you didn't tell about how you got the information about this heterodimer. I believe you have just checked the invert sequence similarity. If not, give the template(s) you have considered. For sure there is a solution. I have seen such data and got reasonably high accuracy on it. Your target sequence length is very high making it a a difficult target. But some methodologies you can apply to see it.
Good Luck,
Ashish
----- Original Message -----
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To: "modeller usage" <>
Sent: Friday, March 5, 2010 3:21:49 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 9, Issue 31
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Today's Topics:
1. Re: special restrains for aromatic packing interactions
(Modeller Caretaker)
2. Re: Windows 7 (Joel Tyndall)
3. Re: Solving modeller problem-reg (Modeller Caretaker)
4. HETERODIMER GENERATION (Ajeeta kaushiki)
----------------------------------------------------------------------
Message: 1
Date: Wed, 03 Mar 2010 07:51:37 -0800
From: Modeller Caretaker <>
To: Thomas Evangelidis <>
Cc:
Subject: Re: [modeller_usage] special restrains for aromatic packing
interactions
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/2/10 11:19 AM, Thomas Evangelidis wrote:
> With respect to my second question, how long do you advice me to set the
> distance between 2 atoms that are supposed to form an H-bond?
We use 3.5A in our own code, but I recommend you try some
reasonable-looking values and look at your results for artifacts.
Ben Webb, Modeller Caretaker
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------------------------------
Message: 2
Date: Thu, 4 Mar 2010 16:06:27 +1300
From: Joel Tyndall <>
To: Tom Venken <>,
"" <>
Subject: Re: [modeller_usage] Windows 7
Message-ID:
<>
Content-Type: text/plain; charset="iso-8859-1"
I have installed it ...shouldn't be any issues. Just try it. Pretty sure it will work. ( ican test it if you really want)
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box?56 Dunedin 9054
New Zealand??
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http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
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-----Original Message-----
From: [">mailto:] On Behalf Of Tom Venken
Sent: Wednesday, 3 March 2010 10:51 p.m.
To:
Subject: [modeller_usage] Windows 7
Hello,
At our university we are in the process of migrating our computers from Windows XP to Windows 7. I found no information about the compatibility of Modeller with Windows 7 in the release notes and I couln't find anything in the mailing list either. So does anyone know if Modeller is compatible with Windows 7, i.e. if someone has tested this OS?
Kind regards,
Tom
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Message: 3
Date: Thu, 04 Mar 2010 08:13:32 -0800
From: Modeller Caretaker <>
To: ithaya raja <>
Cc:
Subject: Re: [modeller_usage] Solving modeller problem-reg
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2/28/10 8:40 AM, ithaya raja wrote:
> I did align my target to the template by using align2d command the
> alignment file had been successfully created. executing py model script,
> it is showing mod9v7.exe error sending report and the modeller
> simultaneously stopped. So i need your help to understand the problem
> what could be? and let me know how to solve the problem else any other
> alternative...?
It sounds like you are on a Windows system, and the Modeller binary
crashed. This could be due either to a problem with your machine's
hardware (e.g. faulty memory) or a bug in Modeller. You can check for
bad hardware by trying the same script on a different machine. If that
still crashes, it's likely a bug in Modeller - in that case I would need
to be able to reproduce the problem in order to fix it, so would need
you to send me exactly the same input files you're using when the crash
occurs.
Ben Webb, Modeller Caretaker
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http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 4
Date: Fri, 5 Mar 2010 15:21:47 +0530
From: Ajeeta kaushiki <>
To:
Subject: [modeller_usage] HETERODIMER GENERATION
Message-ID:
<>
Content-Type: text/plain; charset="iso-8859-1"
Hi
I have to generate a hetero dimer . The entire length of protein is 1500
amino acid . The first dimer is from 150-410 aa and next one is from
786-1188 aa , I have modelled this two domains separately , Now I have to
map it on a known Homo Dimer present in the template pdb to generate as a
heterodimer . Kindly guide or is there any other way to merge the
coordinates .
Thanks & Regards
Ajeeta
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