Re: Symmetry operations

From: \ (jonathan_at_ibt.unam.mx)
Date: Thu Sep 02 2004 - 21:44:39 CDT

Hello. Yes, by doing that we would restrain the monomers to evolve
concomitantly, but we have reasons to believe it might be biologically
relevant in our case, so we are still considering this option.

By the way, in my original post I should have obviously refered to a "pi
rotation", instead of a "reflection". Sorry about that.

Best regards.

J. Valencia.

Quoting Aaron Oakley <oakley_at_rsc.anu.edu.au>:

> I would say that imposing such restraints
> may be desirable for a crystal structure (where
> increasing the observation to parameter ratio helps
> improve the accuracy of the final structure)
> but is not appropriate for an MD simulation,
> where differences between monomers might tell you
> something about the protein.
>
> aaron++
>
> On 25/08/2004, at 4:58 AM, J. Valencia wrote:
>
> > e you would in CHARMM), so the monomer
> > would behave as if it were in the biological unit, without having to
>
> > actually
> > simulate all the atoms in the hexamer. The aim is to save on
> computer
> > resources, since I will be running some relatively long simulations.
> >
> > Any more suggestions will be appreciated.
> >
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