Re: [modeller_usage] loop missing in a crystal structure
To: Modeller Caretaker <>, Modeller Usage <>
Subject: Re: [modeller_usage] loop missing in a crystal structure
From: flavio seixas <>
Date: Tue, 8 Apr 2014 09:27:37 -0700 (PDT)
Reply-to: flavio seixas <>
Hi, Thank you for the reply
I have already considered that option. However, generating models aligned with structure A does not make a model identic to structure A. In another words, I do not want to lose the experimental information that structure A brings, just want to build the missing regions in crystallographic structure A, as it appears in structure B.
Is it possible?
Regards,
Flavio
------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br
On Monday, April 7, 2014 10:34 PM, Modeller Caretaker <> wrote:
On
4/5/14, 8:05 AM, flavio seixas wrote:
> I'm interested in using a crystal structure deposited in the PDB > (structure A). However, there are two important loops missing. > There is another homologous structure B from another source organism, > where those loops are well defined inside electron density. I like to > use the experimental data from this template B to model the missing > loops in the structure A.
Why not just model using both structures as templates? If you're worried that structure B will "mess up" the model in the non-loop regions, align it just with A in those regions and just with B in the loop regions.