As Webb has told. Follow that and you may use these to get good models. 1. Generate maximum possible model number. 2. Try to look for multiple templates for your target sequence. 3. Try to see the alignment file, if your model lacks the conserved sequence information somewhere resulting in complete loss of fold, locally at some place. 4. Try to assess models with all the means provided and then select the best model. Don't rely on any single assessment test. 5. Refinement is not of any usage if you are trapped in local minima earlier in the Potential Energy Surface topological curve.

Good Luck, Ashish

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Tuesday, May 11, 2010 7:37:36 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 9, Issue 74

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Today's Topics:

1. Re: How to optimize a Homology model. (Modeller Caretaker) 2. How to generate Homology models using a computer farm (Caio Veloso) 3. Re: How to generate Homology models using a computer farm (Modeller Caretaker) 4. how to extract the part of structure from a complex ? (Yue)

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Message: 1 Date: Mon, 10 May 2010 07:46:44 -0700 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] How to optimize a Homology model. To: Harish Reddy harisredy@gmail.com Cc: modeller_usage@salilab.org Message-ID: 4BE81C54.9020405@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 5/7/10 7:42 PM, Harish Reddy wrote: > I need some help with optimization. I am confused what to do.

Your best option is to build more models, assess them, and choose the best one (or change your alignment/template if none of the models are acceptable). You would be better off doing this with Python scripts, as the old Modeller TOP scripts are no longer documented or supported.

> On the first instance i used the scrip one to build the models. As i was > not satisfied with the structural quality of the models, i used the > second script below where i included a refinement command. Even then i > couldn't get good models. So, i tried to a optimization script (third)

Actually, all your scripts do the same thing - they call the regular modeling procedure. You have changed the amount of refinement and the optimization parameters slightly, but this does not usually have a large influence on the output models.

> But that > script just kept on failing. So, I am not sure what the problem is..

I can't tell what the problem is either! What do you mean by "the script just kept on failing" ?

Ben Webb, Modeller Caretaker