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" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org 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)

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Message: 1 Date: Tue, 29 Nov 2011 12:22:25 -0800 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] Refine part of an existing model To: flavio seixas oivalf_nix@yahoo.com, Modeller Queries modeller_usage@salilab.org Message-ID: 4ED53F01.2020907@salilab.org 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