Dear Alex,
It is pretty simple.
Simplest way is to make the alignment file with your loop region well aligned to corresponding chunk in structure B and for other residues, put gap in your alignment file for structure A, corresponding to respective additional residues in structure B.
You may use the PRALINE alignment to do it and pipeline that to MODELLER.
There is one more way too to consider the environmental effects on structural topology of A as per the structure B.
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Tuesday, November 1, 2011 9:31:40 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 134
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Today's Topics:
1. Homology Modeling of the Loop (Alexander Predeus)
2. Re: modeller_usage Digest, Vol 10, Issue 132 (Ashish Runthala)
----------------------------------------------------------------------
Message: 1
Date: Mon, 31 Oct 2011 15:02:46 -0400
From: Alexander Predeus <>
Subject: [modeller_usage] Homology Modeling of the Loop
To:
Message-ID:
<CADvsxO=iHEGXCyUW=>
Content-Type: text/plain; charset="iso-8859-1"
Hello all,
I'm very much a beginner at modeling, and this question might be very
trivial. I hope you still would hint me about the answer, for it would help
me a lot.
I have a large protein (say 1500 residues, let's call it protein A) and its
homologue (protein B) of about the same size. Both proteins have published
crystal structures.
Both proteins have a key structural element, loop L. The loop is poorly
resolved in structure A, but well resolved in homologous structure B.
Now, I can take just the L loop regions as separate PDB files from both A
and B and do homology modeling of A based on B; this works really well. But
I also would like the model to consider the surroundings (the rest of the
structure) when evaluating the energies.
Thus, I'd like to keep the REST of A's crystal structure intact, and only
model loop L based on the structure of the same region in protein B.
How can I achieve that?
Thank you in advance!
- Alex Predeus
Michigan State University
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Message: 2
Date: Tue, 1 Nov 2011 09:16:36 +0530 (IST)
From: Ashish Runthala <>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 132
To: modeller usage <>
Message-ID:
<>
Content-Type: text/plain; charset=utf-8
Dear Junior,
What you actually want to state?
Do you need to build an average model based on the topology of 10 models? For this you may use them as templates without calling the chain identifiers.
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Monday, October 31, 2011 7:46:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 132
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Today's Topics:
1. Re: What is the mistake in this set of lines? (Ashish Runthala)
2. Re: What is the mistake in this set of lines? (Ashish Runthala)
3. Build a model with multiple models (junior)
----------------------------------------------------------------------
Message: 1
Date: Sat, 29 Oct 2011 10:39:22 +0530 (IST)
From: Ashish Runthala <>
Subject: Re: [modeller_usage] What is the mistake in this set of
lines?
To: modeller <>
Message-ID:
<>
Content-Type: text/plain; charset=utf-8
Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code.
How these variables are declared in MODELLER?
Thanks
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "Ashish Runthala" <>
To: "modeller" <>
Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: What is the mistake in this set of lines?
Dear Modellers,
I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder.
The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder.
MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID.
So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template.
So what is the mistake in this set of lines? How should i solve this task.
for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'),
(pdbfile,pdbfile,fileName,'A')):
mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain))
aln.append_model(mdl, atom_files=code, align_codes=atomfile)
Thanks,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
------------------------------
Message: 2
Date: Sun, 30 Oct 2011 15:52:37 +0530 (IST)
From: Ashish Runthala <>
Subject: Re: [modeller_usage] What is the mistake in this set of
lines?
To: modeller <>
Message-ID:
<>
Content-Type: text/plain; charset=utf-8
What nobody knows to declare such data types? Any guesses with anyone what it should be, as probably there in MODELLER modules and functional binaries.
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "Ashish Runthala" <>
To: "modeller" <>
Sent: Saturday, October 29, 2011 10:39:22 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: What is the mistake in this set of lines?
Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code.
How these variables are declared in MODELLER?
Thanks
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "Ashish Runthala" <>
To: "modeller" <>
Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: What is the mistake in this set of lines?
Dear Modellers,
I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder.
The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder.
MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID.
So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template.
So what is the mistake in this set of lines? How should i solve this task.
for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'),
(pdbfile,pdbfile,fileName,'A')):
mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain))
aln.append_model(mdl, atom_files=code, align_codes=atomfile)
Thanks,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
------------------------------
Message: 3
Date: Mon, 31 Oct 2011 06:16:22 -0800
From: junior <>
Subject: [modeller_usage] Build a model with multiple models
To:
Message-ID:
<CAEJMx6wtgQ8U6MAG+>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
How do I build a PDB file containing more than 10 models?
Thank you.
Sam Kauba
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