Note, however, that Modeller models generally do not need refinement
(and if they do, using Modeller to do it probably won't make the models
any better!)
Sorry to say sir benn, but MODELLER do refine the models to some extent if the mutual orientation of individual domains in a multi-domain structure or the initial models's topology is correct and parallel to the actual native structure. But all this fun of pulling the models closer to native state works well only when the correct model decoy is correctly selected for.
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, November 30, 2011 7:32:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 148
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Today's Topics:
1. Re: Refine part of an existing model (Modeller Caretaker)
2. Is there any Modeller Script to refine unaligned loop chunks
(Ashish Runthala)
3. Enc: Error with import os (Bruno Madio)
----------------------------------------------------------------------
Message: 1
Date: Tue, 29 Nov 2011 12:22:25 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Refine part of an existing model
To: flavio seixas <>, Modeller Queries
<>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 11/29/2011 03:03 AM, flavio seixas wrote:
> I was studing Modeller manual and I am not sure if there is a routine
> in modeller that can refine only part of an existin model, like loop
> refinement do.
Just build a new comparative model using the regular automodel class,
using your original model as the template. Use a simple alignment
containing two copies of the model sequence. Override select_atoms() as
per the example at
http://salilab.org/modeller/9.10/manual/node23.html
to define the region to refine.
Note, however, that Modeller models generally do not need refinement
(and if they do, using Modeller to do it probably won't make the models
any better!)
> However, the region that I am interested to refine is
> not a loop. Because of this, I can not use loop refinement in helical
> segments, even though a region of three residues.
Loop refinement can be used for any region without a template. The
protein can adopt any secondary structure, including an alpha helix. But
yes, typically loop refinement will give you coil structures.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Wed, 30 Nov 2011 15:02:09 +0530 (IST)
From: Ashish Runthala <>
Subject: [modeller_usage] Is there any Modeller Script to refine
unaligned loop chunks
To: modeller <>
Message-ID:
<>
Content-Type: text/plain; charset=utf-8
Dear Modellers,
Though there are many problems in modeling the loop regions, but even when there is no insertion in the loop region and is devoid of any higher order localized structural topology, the loop residues are just connectors. Here also i am seeing some problem.
Even when the periphery is at a minimal distance threshold to native state making the GDT_TS or even GDT_HA very high, the RMSD i found was much more than expectation. So the model scrutiny revealed the complexity in the loop region.
SO IS THERE ANY SCRIPT IN MODELLER WHICH REFINES ALL LOOP CONNECTORS THROUGH MD CONJUGATED GRADIENT, MAKING THE RMSD ALSO DROOP DOWN AS IS THE CASE FOR GDT OR TM-SCORE.
Thanks a lot,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
------------------------------
Message: 3
Date: Wed, 30 Nov 2011 05:48:11 -0800 (PST)
From: Bruno Madio <>
Subject: [modeller_usage] Enc: Error with import os
To: "" <>
Message-ID:
<>
Content-Type: text/plain; charset="iso-8859-1"
Dear Modeller,
When I try to do anything with modeller9.10, an error menssage occurs with "C:\Program Files (x86)\Modeller9.10\modlib\modeller\__init__.py" line 51 and?I can?t ?import "os" from "C:\Program Files (x86)\lib\os.py" line 106.
Please, could you help me fix this bug?
I have read the release notes, but I still could not fix the error. Could you teach me step by step?
All the best,
Bruno Madio
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