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Re: [modeller_usage] loop missing in a crystal structure



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.

    Ben Webb, Modeller Caretaker
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