Subject: Re: [modeller_usage] building missing residues
From: Modeller Caretaker <>
Date: Tue, 09 Apr 2013 16:56:49 -0700
Cc:
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.