[Chimera-users] Denaturing a protein

[Nadir T. Mrabet]

Why is that?
Simply, because the denaturate state is difficult to define as it 
certainly correspond to a multitude of conformations including some of 
the native state.

Pr. Nadir T. Mrabet
Structural & Molecular Biochemistry
N-gere - INSERM U-954
University of Lorraine, Nancy
School of Sciences and Technologies
& School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax:   +33 (0)3.83.68.32.79
E-mail: Nadir.Mrabet <at> univ-lorraine.fr
Cell.: +33 (0)6.11.35.69.09

LEGAL NOTICE
Unless expressly stated otherwise, this message is confidential and may
be privileged. It is intended for the addressee(s) only.
Access to this E-mail by anyone else is unauthorized.
If you are not an addressee, any disclosure or copying of the contents
of this E-mail, or any action taken (or not taken) in reliance on it,
is unauthorized and may be unlawful.
If you are not an addressee, please inform the sender immediately.

On 14/09/2012 19:56, Elaine Meng wrote:
> Hi Vamsee,
> Sorry no, there is no way to do those kinds of calculations in Chimera.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Sep 13, 2012, at 6:31 PM, vamsee wrote:
>
>> Hi Elaine,
>> Thanks for the answer for the previous question. I am back with one more :)
>>
>> Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera?
>> Thanks again
>> Vamsee
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>