Re: [modeller_usage] building missing residues

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 4/8/13 2:22 AM, Mary Varughese wrote:
> a protein i am dealing with has some missing residues. I am trying to
> build it with modeller. How could i verify the structure generated?

This is simply a comparative model, where the structure with the missing 
residues is your template. So you'd verify the structure in the same way 
as any other comparative model, e.g. using an assessment method such as 
normalized DOPE.

> Also the remarks says, CA 5% of the side chains are poorly defined and
> are currently modelled as alanines.

If the correct sequence is available in the SEQRES records, you should 
probably use that in your model.

	Ben Webb, Modeller Caretaker
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